Sonar4 and Sonar5-Pro

Post processing systems

Operator manual version 6.0.3

Biomass estimation, Tracking, Macrophyte, Multi freq. Multi beam, Dynamic

sound profile, Data insight, Classification, Statistics, Maps, Pictures,
Crossfilter, Single echo, Bottom and water current detection, Fish sizing,
Oscilloscopes, 3D-Amp and phase diagrams, Ray tracing, Transducer
position prediction...........

Balk and Lindem 30.12.2014

NORWAY
SonarX. Default setup for biomass estimation as described in chapter 8.

SonarX. Horizontal approach. Simple tracking setup with additional windows added from
the Analysis->1-Setup menu (chapter 4 and 12). The track's exact positions relative to the
bottom profile and the river surface is seen in the lower left position diagram. The position
diagram in the lower center part display the sound beam as seen from a bird's view. Red
lines indicate the direction and strength of the water current. The chart to the right can
display all the tracks features as a function of time. At the moment the echo intensity is
displayed. Stable TS values are seen within the -3 dB beam while erroneous off-axis
compensation is observed outside the beam.

i
Sonar 5-Pro Setup for auto tracking as described in chapter 12. Here Echogram window
in SED-display mode with Event lines, Tracker, Classification window, one position
diagram and the advanced parameter dialog's description page.

Sonar 5-Pro. Study echoes in a layer with oscilloscopes (chapter 16) and the 3D-
echograms (chapter 17)

iii
Fish tracking in data from a horizontally aligned transducer in a river. The Amp echogram
threshold has been set to presents the entire echo intensity in order to see background
reverberation. In noisy environment the background reverberation gives important
information for the interpretation of tracks. Three position-diagrams have been opened to
study the tracks true position in the river relative to the bottom profile, relative to the
water current and relative to the cross section of the beam. It is clearly seen that the track
moves against the water current. The track info dialog in the lower right corner is set up to
present the individual echo positions. The advanced parameter dialog opened at the
description page is placed in the upper right corner to present pictures and text notes from
the survey. Additional comments and notes can be added here during the analysis. The
example file can be found in the folder: Balk_Lindem\Sonar demo files\Rivers\Tana of the
installation CD.

v
Sonar5-Pro set up to work with a 6 frequency recording of herring and mackerel. The
Frequency response function indicates that the analyzed school is mackerel. Each
echogram can be operated individually or linked to the other echograms so that zooming in
one echogram zoom the other as well. One echogram can be filtered and subtracted from
another with another frequency and echograms can be applied as thresholds to other
echograms. Classification maps and RGB-echograms are available as well.

vii
Acknowledgement
SonarX would not have been what it is today had it not been for the help from many
different persons contributing with suggestions for new methods and improvements of
existing tools, for help with testing and for providing test data.

First of all we want to thank dr. Jan Kubecka and his team and students at the
Hydrobiological Institute, Academy of science of the Czech Republic, Ceske Budejovice.
Without Dr. Kubecka and his team SonarX would never have have been what it is today.

Simrad AS with their staff has been of great help with theoretical and practical support. In
particular, we will like to thank Frank R. Knudsen, Haakon Solli and Helge Bodholt for
their assistance.

BioSonics, Sound Metrics Corp, MacArtneyAS, and HTI have been very helpful with the
development answering questions and providing background documentations for theire
echosounders and data formats.

An important milestone in the development was the inclusion of the Software Guided
Analysis (SGA). This work was higly supported by dr. Lars Rudstam and the Study Group
on Fisheries Acoustics in the Great Lakes.

Other people who have contributed significantly are Marc Schmidt from
Landesfischereiverband Westfalen und Lippe e.V. (Ge), Georg Rakowitz from the
University of Vienna (Au), Karl Øystein Gjelland at the institute of aquatic biology at the
university in Tromsø Norway, Jan Kemper from the Organization for the Improvement of
Inland Fisheries in Netherland.

Test data have been of great importance. We have recorded data and performed
experiments in the field for years. Data from other scientists have, however, played an
important role in the development. Some of these data are available on the SonarX CD. We
will thank every one that has contributed. Especially we want to thank Jean Guillard and
Nathalie Gaudreau (Ca), Dan Yule (US), Atso Romakkianemi (Fi), Juha Jurvelius (Fi), Pia
Romare (Se)

Experiments in the field

ix
Reference to this software
For reference to this software, press the programs top menu Help=>About. The reference
will then automatically be copied to clipboard.

What can SonarX do

Sonar5-Pro has all the option. For Sonar4, tools related to standard biomass estimation,
macrophyte estimation and simple tracking are available.

Pre-analysis
 Single echo detection
 Bottom detection. (Enhanced with image analysis)
 Max range detection
 Dynamic sound speed and alpha correction
 Passive noise subtraction
 Heave correction
 Manual noise erasing tools
 Automatic noise reduction systems, unwanted target removal
 Water current detection

Analysis
 Biomasse estimation
 Tracking and tracing
 Macrophyte
 Seabed class.
 Track statistics
 Image analysis
 Multi frequency analysis
 Synchronized echograms with DIDON movies
 Export of bathymetric data

Data insight
 3D-echogram
 Oscilloscope
 DIDSON movie player
 Frequency response function, classification maps and RGB echograms
 TS range distribution, Size distribution,
 Integrams
 SED detections versus off axis angle

Interpretation
 Fish database
 Catch data
 TS to weight and length calculator

xi
  Track aspect TS correction
 De convolution for estimation of size when aspect is unknown
 Ray tracing for estimation of targets and beam in hor. app.

Presentation
 Transect maps
 Tracked echoes in all aspects
 Tracks relative to surface and bottom profile (horizontal app.)
 Tracks relative to water current (horizontal app.)
 Photos, drawings and maps
 Free threshold.
 Free color per dB scale
 Time, ping number, and range
 Geographical positions and sailed ship distance.
 Zoom in and out
 Layers: Pelagic, Bottom, Free number of sub layers and sub segments

Noise
 Manual and automatic noise removal systems
 Noise filtering
 Target noise separator.
 Track filtering
 Passive noise subtraction

Editors
 Noise editor
 Bottom editor
 Text editors (txt, rtf)
 Bottom profile editor
 Water current editor
 Graphical transducer positioning tools
 Event notes editor and browser

File overview and file opening

 Simple file open dialog presenting only filenames
 Advanced file open menu presenting filenames with record number, survey
description, transect description, additional text description and photos.
 Graphical presentation of transects in digital maps.
 Opening of echograms at positions selected graphically from maps
 Quick file change functions.

SonarX background
SonarX is based on the findings from the Dr. Sci. study (Balk, 2001) Development of

xii
hydroacoustic methods for fish detection in shallow water. The thesis is available on the
installation CD and in the program folder if installed.
Mail to: Helge.Balk@fys.uio.no Home page: www.fys.uio.no/~hbalk

xiii
Tutorials
See the file 0_Tutorial_Start.Doc in the folder Help_Tutorials

Topics not directly seen in the list of chapters

Topics Chapter Section
Bottom, bottom detection, bathymetry 2 Bottom
Calibration 2 Utility menu
Connecting additional data such as trawling and 21 Survey map and events
CTD
DIDSON multi beam 4 Didson viewer
Exporting data 2 Export data
Files and folders: Move, copy, delete rename, etc.. 3 Survey and file manager
Files, merging files 5 Merging files
Files, Multiple files 2 Working with multiple files
GPS, Navigation, NMEA, maps 2 Navigation, GPS and NMEA,
Survey Menu
Layer, Pelagic, Bottom 4 Layers
Macrophyte analysis 4 Macrophyte analysis
Menu, File, Echogram, Analysis, Utility, Survey, 2 Main menu
Help
Noise, erasing echoes, passive noise, unwanted 6 Noise
targets
Quality, SED quality 11 single echo quality
Seabed calssification 4 Seabed classification
Single echo detection (SED) 4 Single echo detection
Thresholds (Basis, Working, Warning) 8 Thresholds
Tracking, Storing tracks 4 Tracking and counting
TVG 2 TVG and sonar equations

Calculations
Most calculations are presented in chapter 08_Biomass See also

What Chapter Section

Power, TS, Sv Sonar equations, TVG, correction 5 Sonar equations
factors
Single echo detection 4 Single echo detection
Track features 11 Track feature calculations
Biomass estimation methods 8 Biomass estimation methods
Volume and area of the beam 8 Volume and area observed by
one ping
Observed volume and area along a transect 8 Volume and area observed by a
moving transducer

xv
Trouble shooting
Problem Ch Section
.
Analysis: Nothing happen when I select a region to 6 Overruled or rejected requests
analyze.
Transects: Why do I not see the transect lines in the 3 Trouble shooting
advanced file open dialog?
Bottom: Why do I not see the bottom line in the 6 Why do I not see the bottom line?
echogram?
Layer: Why do I not see the layer lines? 4 Why do I not see the layer lines?
Echogram: Why do I not see the Echogram? Why 6 Troubleshooting
does the colors look so strange?
Navigation 2 NMEA error handling

xvi
Contents

PART I ............................................................................................................................................................ 19

01 INTRODUCTION .................................................................................................................................... 21

02 GETTING STARTED .............................................................................................................................. 27

03 ADVANCED FILE OPEN DIALOG ...................................................................................................... 49

04 ANALYZING DATA ............................................................................................................................... 59

05 CONVERTING FILES .......................................................................................................................... 107

06 ECHOGRAM WINDOW ...................................................................................................................... 141

07 ECHOGRAM CONTROL DIALOG .................................................................................................... 159

08 BIOMASS WINDOW ............................................................................................................................ 179

09 POSIGRAM AND TRACK INFORMATION ..................................................................................... 227

10 SONAR PARAMETER DIALOG ........................................................................................................ 239

PART II ........................................................................................................................................................ 259

11 SYSTEM CONFIGURATION DIALOG ............................................................................................. 261

12 TRACKING ............................................................................................................................................ 293

13 CLASSIFICATION ................................................................................................................................ 313

14 FISH BASKETS ..................................................................................................................................... 327

15 IMAGE ANALYSIS ............................................................................................................................... 339

16 THE OSCILLOSCOPE WINDOW ...................................................................................................... 369

17 3D-ECHOGRAM WINDOW ................................................................................................................ 381

18 SAMPLE DATA ANALYZER .............................................................................................................. 395

19 CROSSFILTER DETECTOR ............................................................................................................... 399

20 SINGLE ECHO DETECTOR TEMPLATE ........................................................................................ 417

21 SURVEY AND EVENTS ....................................................................................................................... 425

22 SOUND PROPAGATION AND RAY TRACING .............................................................................. 435

23 MULTI FREQUENCY ANALYSIS ..................................................................................................... 445

24 MULTI BEAM ANALYSIS (DIDSON)................................................................................................ 463

REFERENCES ............................................................................................................................................ 479

Balk and Lindem 17

18 Balk and Lindem
 Part I

SONAR4
SONAR5-Pro

SonarX

Balk and Lindem 19

01 Introduction
Main menu

ABOUT THE SYSTEM ................................................................................................................................................21

ABOUT THE MANUAL ...............................................................................................................................................21
Hyperlinks ..........................................................................................................................................................22
SYSTEM REQUIREMENTS ..........................................................................................................................................22
Important notes. Please read this! .....................................................................................................................22
INSTALLATION .........................................................................................................................................................22
Installation from CD ..........................................................................................................................................22
Manual installation ............................................................................................................................................22
Upgrading the software......................................................................................................................................22
Notes about short keys .......................................................................................................................................23
UNINSTALL ..............................................................................................................................................................23
LICENSE ...................................................................................................................................................................23
License driver .....................................................................................................................................................23
HISTORY OF SONARX ..............................................................................................................................................24

About the system

Sonar4 is mainly a biomass estimation tool, while Sonar5 is a state of the art system with a
vast number of methods and tools.

Sonar5 has been designed to fulfill three main tasks

a) Abundance estimation, (biomass estimation and counting)
b) Species behavior studies such as avoidance and
c) Physical studies such as sound propagation etc.

About the manual

This manual covers the Sonar4, Sonar5-Pro post processing systems or SonarX for short.
The first part covers both programs. The second part covers mainly additional functions
available in Sonar5.

The manual is available in a PDF file intended for printing. The PDF file is located in the
folder: \Balk_Lindem\Manual.

An interactive version of the manual is available in the folder: \Balk_Lindem\ Program\

Help_doc. The doc files serve as help files for the program. As an example, requesting help
when the echogram window is active opens the file named 06_Echogram.doc in a Word
browser. The interactive manual can also be read by opening the top file:
00_Main_Menu.doc. This file connects the chapters by hyperlinks. Alternatively, opening
00_Manual_Master.doc will open the manuals master document. From the master
document, searching through all files for a topic may be a help if the topic is difficult to
find with other methods. .

Chapter 1 contains information about installation, license, and history. Chapter 2 gives a

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01 Introduction SonarX Operator Manual
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general overview of how to operate the system, and where to find more information.
Chapter 4 covers the analysis menu and analysis methods, while the remaining chapters
describe windows and dialogs dedicated to special tasks.

Hyperlinks
Hyperlinks are jump points bringing the reader to related topics. Two kinds of hyperlinks
are applied. They are page numbers and blue text. In the electronic version of the manual,
clicking on a page number or a blue text, open the manual at that topic.

System requirements
SonarX has been deigned to run under modern Window platforms such as Win98, WinNT,
WinME, Win2000 and WinXP. It has been developed on a 300 MHz Best laptop with a
13" TFT screen running Win98.

Important notes. Please read this!

a) Only one copy of the program may be run at a time. Any attempt to start a second
copy will be aborted.
b) The program has to be run from a disk with write access like the C drive. Errors may
occur if it is run from a write-protected medium such as a CD.
c) When copying files from a CD to the hard disk, the files will automatically be marked
as write protected. SonarX will tempt to change the protection. NT and XP based
platforms may refuse this if one is not logged on with administrator rights. If not,
one will have to turn off the write protection manually. The installation program turns
of the write protection automatically when it copies files from the installation CD.

Installation
Installation from CD
Inserting the SonarX CD in the PC will normally auto-start the installation program. If not,
locate and start the program named Contents.exe on the CD’s root. Starting this program
and clicking the install button will install the system. The Contents.exe program does also
provide background information, articles and uninstall options.

Manual installation
The SonarX programs have been written as stand alone applications. No special
installation procedure is needed. Simply copying the Sonar4.exe or Sonar5_Pro.exe file to
a folder on one of the PC's hard disks is sufficient. Clicking the program icon will start the
program. Refer to the paragraph "License" if a license driver is to be installed manually.

Upgrading the software

New methods and improvements will be implemented in the systems. Hence, it may be an
idea to check for new upgrades now and then. This can be done with the programs main

22
Operator Manual SonarX 01 Introduction
_________________________________________________________________________

menu: Internet. Upgrades can be downloaded through the net. No tedious uninstall
procedures followed by sophisticated installation procedures are needed. Simply replacing
the original .exe file with the new downloaded file is sufficient.

Help files
Help files are written as separate files. The program expects to find the files in one of the
following folders :\Balk_Lindem\Program\Help_doc or \help_rtf. For upgrading the
manual and help files, replacing the old files with the new one is sufficient.

Additional tools
Some of the tools found in the programs tool menu are written as separate exe files. They
have to be copied to the same folder as the SonarX.exe program to be accessible from
SonarX.

Notes about short keys

A window shortcut consists of two pointers, one pointing to the program folder and one
pointing to a start folder. For SonarX, both pointers must point to the program folder. If
not, the program will not be able to locate the help and tool files. Short keys can be made
from Windows Explorer with the right mouse button. To start Explorer, press the right
mouse button on Window's Start button. See a Window manual for more information on
short keys.

Uninstall
The program does not tamper with any of the PC's system files or registry entry. Hence,
simply deleting the program folder will result in a total cleanup. See the paragraph
"License" to remove the license driver if installed.

License
All parts of the program except the converter are free to use. The program and converted
files can be copied and analyzed without any restriction. A Dongle (Hardware lock) has to
be connected to the pc's parallel port or USB port to run the converter. To test the program,
a demonstration Dongle with a limited number of conversions is available. Alternatively,
files can be sent to us for conversion through Internet or by mail. A library of converted
files is available on the installation CD.

License driver
To make the connection between the sonar program and the Dongle, a window driver is
needed. Installing is done by the SonarX installation CD. The driver can also be installed
manually. To do so, copy the folder “\Balk_Lindem\Program\licence” to one of your hard
disks and run the setup.exe program located in the licence folder. See the readme file in the
licence folder for more information.

23
01 Introduction SonarX Operator Manual
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History of SonarX
SonarX have been developed by Helge Balk and Torfinn Lindem. The programs are
designed for sonar data post-processing. The development started during a fieldwork in the
river Tornionjoki in northern Finland summer 1997. As an introduction to the PhD-study:
"Development of hydroacoustic methods for fish detection in shallow water" (Balk 2001),
we wanted to compare the data from Simrad's EY500 with data from HTI's Mod 243 echo
sounder. We found that the available software (EP500 and TrackMan) could not do the job.
Files were recorded with different start time and ping rate, and the programs displayed
different kinds of data. Trackman displayed the single echo detection echogram in black
and white while EP500 displayed the amplitude echogram in colors. Comparing data was
simply not possible. Hence, we decided to develop our own software.

We did not start on scratch. A window based echogram viewer had already been developed
as part of the master thesis "Digitizing sonar data" (Balk 1996). In this program we had
studied methods for fast transferring and displaying of large amount of data. The
developed methods were applied as an engine for the new software.

The name Sonar5-Pro came into being simply because it was our 5th version of the sonar
post processing code. It was easier to talk about Sonar5 than to say sonar software version
5 and it soon became a name.

In the beginning it was only Sonar5-Pro. Methods for visualizing data from the echo
sounder were implemented first. We wanted to "see" what was going on in the water and
what was detected by the echo sounders amplitude detector (Amp echogram) and single
echo detector / SED echogram). We spent much effort on implementing methods for fast
access, displaying, zooming, and moving around in the recorded echo data.

In the autumn 1997 we were asked to monitor salmon migration in River Tana (northern
Norway). A test recording was done the same year, and fieldwork was carried out summer
1998 and 1999. In this period Sonar5's tracking, track storage, track statistic and
classification methods were implemented.

During the winter seasons, experiments with sound field were carried out on ice-covered
lakes. We learned that traditional single echo detection frequently failed when the sound
beam was aligned close to a boundary. Hence, we started to develop alternative methods to
the traditional single echo detector.

So far the program had served as a research tool, but the lack of suited post-processing
software resulted in requests from other scientists whether Sonar5 could be made
commercially available. In spring 2001 dr. Jan Kubecka (Cz) asked us to make a user-
friendly version for his institute.

EP60 was born in Sept. 2001 when Dr. Frank. R. Knudsen from Simrad AS asked us write
a special version with methods for biomass estimation, bottom detection and navigation
which could take data from their new EK60 echo sounder. This version should be easy to
use. Since many of the users where familiar with the DOS based EP500 program, it was
decided to make the program as identical as possible. To reduce the amount of
programming the requested methods where first implemented in the existing Sonar5. Then

24
Operator Manual SonarX 01 Introduction
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Sonar5 was given an EP500 look. In the end, all but the requested analysis methods where
disabled from EP60.

During the year Simrad and many other tested the program and in October 2002 the
program was accepted for sale. As part of this deal the name was changed from EP60 to
Sonar4.

Since then a steady stream of suggestions from the steady increasing number of users has
resulted in a system supporting a vast number of applications, and providing a rich library
of tools.

In 2005 multi frequency applications started to be popular using 2..6 frequencies for
species classification. This demanded a software engine capable of handling information
from multiple files simultaneously. Sonar6-MF was created to do this. Sonar6-MF served
as an experimental and test tool for multi-frequency from 2005 to 2007 when we felt
confident in it. In January 2007 Sonar5-Pro was upgraded to Sonar6-MF standard and the
Sonar6-MF project was closed.

25
02 Getting started
Main menu

MY FIRST RUN .........................................................................................................................................................27

GETTING HELP .........................................................................................................................................................28
BOTTOM ..................................................................................................................................................................29
Bathymetry .........................................................................................................................................................29
Bottom profiles for fixed, horizontal applications ..............................................................................................30
CHARTS ...................................................................................................................................................................31
FILES, FOLDERS TELEGRAMS AND PROJECTS ............................................................................................................32
Files in a sonar project ......................................................................................................................................33
Sonar source files to be converted .....................................................................................................................33
Files types used by the system ............................................................................................................................33
Control files .......................................................................................................................................................34
Telegrams ...........................................................................................................................................................34
Two different Co-ordinate systems .....................................................................................................................35
OPENING FILES ........................................................................................................................................................35
Standard file open dialog ...................................................................................................................................35
Advanced file open dialog ..................................................................................................................................36
Reopen dialog ....................................................................................................................................................36
Working with multiple files and Quick file change functions .............................................................................36
NAVIGATION, GPS, UTM AND NMEA ....................................................................................................................37
PARAMETERS ...........................................................................................................................................................38
EXPORTING DATA ....................................................................................................................................................39
PRINTING ECHOGRAMS ............................................................................................................................................40
THE MAIN MENU ......................................................................................................................................................40
File menu ...........................................................................................................................................................41
Echogram menu .................................................................................................................................................42
Analysis menu ....................................................................................................................................................42
Utility menu ........................................................................................................................................................43
Stop menu ...........................................................................................................................................................44
Survey menu .......................................................................................................................................................44
Internet menu .....................................................................................................................................................45
Help menu ..........................................................................................................................................................45
TVG AND SONAR EQUATIONS ..................................................................................................................................45
Changing TVG ...................................................................................................................................................46
UNDERSTANDING WINDOWS ....................................................................................................................................46
Splitter ................................................................................................................................................................47
DEMONSTRATION FILES ...........................................................................................................................................47

My first run
When the program is started, the program logo will be displayed and then the program will
open and display an example echogram file located in the program folder. If the example
file has not been installed, the message- “File not found” will appear and an empty
echogram window will be seen.

If the echogram window is empty, the first thing to do is to open a converted sonar file.
E.g. one of the demonstration files. To do so, select the File open menu. This will activate

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02 Getting started SonarX Operator Manual
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a standard file open dialog. Use this to open a sonar file from the folder "Sonar demo
files".

If the appearing echogram is displayed in a disfavored way, activate the echogram control
dialog from the echogram menu and adjust the threshold, number of colors per dB, range
etc. until the echogram appears in a preferable way. (See chapter 7 Echogram control
dialog)

Activate the echogram window by pointing the mouse to the window's caption and press
the left mouse button. (See chapter 6 Echogram window and the section activating a
window in this chapter)

Select a region by positioning the mouse near some echoes of interest in the echogram
window, press the left mouse button down, move the mouse to a different position and
release the mouse button. (See the section: Draw a rectangle in chapter 6 Echogram
window)

The different visible windows will now handle the selected region. If a tracker window is
opened and set to perform manual or automatic tracking, then tracking will be performed
within the selected region. If a biomass window is opened, then biomass will be estimated
for the selected region. If a 3dechogram window is opened, a 3D-echogram will be
generated displaying the selected region and so on. Analysis and data insight windows are
opened from the analysis menu.

Getting help
All main windows and dialogs have a separate help menu. When a window is activated its
help menu can be accessed in three ways.

a) Pressing the F1 key

b) Pressing the right mouse button and selecting help from the popup menu

c) Selecting help from the programs top menu: Help

Help files are located in the following folders

Balk_Lindem\Program\Help_doc
Balk_Lindem\Program\Help_rtf
Balk_Lindem\Program\Help_Articles
Balk_Lindem\Manual

Minor help files are written in rich text format (rtf) and stored in the Help.rtf folder. These
files are opened and displayed with the program's built-in RTF-browser. The main help
files are written with a Word editor and saved in .doc format in the Help_doc folder. The
Help_Articles folder contains background articles in various formats. If installed,
hyperlinks in the main help files will be able to open these articles. The folder Manual
contains a printer friendly copy of the entire manual in PDF format. A PDF reader can be

28
Operator Manual SonarX 02 Getting started
_________________________________________________________________________

installed from the installation CD. The folder Help_Tuturials contain PowerPoint and word
files intended to give a mainly graphical presentation on how to carry out certain tasks.

Bottom
SonarX provides two different bottom definitions. The first definition is a line restricting
analysis to shorter ranges. The second definition is the bottom profile observed under the
beam of a fixed positioned, horizontally aiming transducer.
1. Bottom line: See Bottom menu in chapter 6, Bottom detector in chapter 4, and layer
and bottom in chapter 7.
2. Bottom profile: See Bottom profile and transducer position in chapter 9 and the
application page in the advanced parameter dialog chapter 10.

Bathymetry
The Bottom line can be exported together with GPS positions, time and ping through clip
board or file. The following two menus start the export

1. Echogram => Export => Bathymetric data. See Export => Bathymetric data in
chapter 6.
2. File => Open advanced => Export=>Bathymetric data. See Bathymetric data in
chapter 3.

Bottom line for vertical and horizontal applications

Figure 1. Bottom line applied to restrict analysis. Left: traditional application of the
bottom line, restricting the analysis to the regions above the bottom. Right: Bottom line
combined with bottom layer applied to restrict analysis in a horizontally recorded file.
The color and thickness of the bottom line are user defined.
The bottom line is a variable line restricting analysis to ranges shorter than the position of
the line. This line will normally be associated with the bottom seen in vertical applications.
Hence, the line is named the bottom line. The line can, however, equally well be applied to
restrict analysis in horizontally recorded files and to other situations with no bottom. The
automatic bottom detector can fit the line to the actual bottom. The mouse can draw a free
hand line to modify the automatically detected bottom or to avoid whatever ranges the
operator might want to avoid analyzing.
Storing the bottom line
Bottom is stored in a separate file. This file has the same name as the echogram file, but
with the extension "bottom". The file is generated by the converter provided that the
original source file (*.dg?, *.raw......) contained bottom information. If not, the bottom file

29
02 Getting started SonarX Operator Manual
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can be generated by entering the menu Echogram => Bottom => Edit bottom. The menu
opens the bottom editor. The editor contains tools for automatic and manual bottom
detection. It is possible to define many different bottom lines and store them for later use.
Controlling the bottom line
The echogram control dialog's layer and bottom controls the appearance of the bottom line
in the echogram. See section Layer and bottom in chapter 7-Echogram control dialog. Line
thickness, color, bottom layer and visibility are controlled here. If the bottom line is
visible, all analysis will be restricted to the region above the bottom line. If a bottom layer
is displayed, analysis will be restricted to the bottom layer. The bottom layer can be
divided into segments, but not into sub layers. To analyze sub layers, the operator must
select a tin layer and analyze it, then lift the layer with the margin parameter and repeat the
analysis.

Why do I not see the bottom line in the echogram?

 The Show bottom line checkbox in the echogram control dialog is not turned on
 The bottom line color is set to the same as the surrounding color
 The thickness of the bottom line is set to a small value so that the line is difficult to see
 The echogram window has been zoomed to show a region where no bottom is defined
 There has not been defined any bottom line or the file containing the bottom definition
does not exist in the same folder as the echogram file.
 All bottom detection is at 0 meter or at max range

Bottom profiles for fixed, horizontal applications

A bottom profile defines the bottom seen under a fixed positioned, horizontally aligned
transducer. If the transducer's position, tilt and bottom profile have been described, the
position diagram will be able to display the sound beam and the fish tracks relative to the
river or lake's water cross section at the site. The track information dialog will be able to
present the exact positions of the tracks and echoes in the water.
Refer to section Bottom profile and transducer position in chapter 9-Position diagram, and
the section named The application page in chapter 10-Sonar parameters for more
information about bottom profiles.
Hint: Placing the transducer in a shallow river or lake can be difficult. To find the best
position and tilt, the bottom profile can be described to SonarX and the operator can play
with the tilt and the transducer position relative to the defined profile. This can help finding
the optimal placement of the transducer system in the river.

Figure 2. Position diagram window in the exact-yz display mode. The surface, beam and
bottom are seen. Tracked echoes from a passing fish are seen near the bottom at Zr=25m.

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Figure 3. The track information dialog presents the exact positions of the echoes seen in
Figure 2

SonarX support two different bottom definitions.

a) The bottom observed under a fixed horizontally aligned transducer.
b) The bottom observed with a vertically aligned transducer.

The Echogram window and the Bottom detector dialog handles bottom seen in vertical
applications, while the Sonar parameter dialog and the Position diagram window handle
bottom in horizontal applications.

Charts

Figure 4. The chart seen in the Biomass window.

Charts are found many places in the program such as in the Biomass window and the Track
information dialog. The chart presents data graphically. Most places where a chart is
found, a control check box can enable or disable the chart control panel seen above the
chart in Figure 4. The panel controls the chart and the way the chart presents the data. The
buttons have the following meaning. The chart has a separate help file named
TeeUser5.hlp. This file is supposed to be found at the same folder as the SonarX program.
Opening the charts edit dialog presents the edit dialog with a help button in the lower left
corner (Figure 5). This button opens the TeeUser5.hlp file.

Rotates the chart

Moves the chart

Zoom

Scale

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Toggle between 3 and 2 dimensional charts

Edit all aspects of the chart from axis to titles and presentation

Print the chart

Copy the chart to clip board

Save the chart to file

Figure 5. The 3D-page in the chart editor

As seen from the above figure there are tabulated pages for a waste number of settings and
we will not present them all here. A few may though be appropriate to mention.

Decimals and number formats: To change the axis labels format open the chart editor
and select the page: Axis=>Left Axis=>Labels=> Format. Here the labels can be set up
with more decimals or tuned to present the results in exponential formats.

Export: Most SonarX windows are equipped with an export menu. However, there may be
situations where one do not find exactly what one wants. Then try the charts editor and
open the export or print page.

Files, folders telegrams and projects

A converted sonar file has the extension dot uuu. The file contains echogram parameters
such as pulse length, frequency etc., together with the actual echogram. The uuu file is the
most important file and the only file needed for the primary operations and analysis. All
other files provide secondary services. Examples of additional files are the bottom file
storing the bottom line, the design file describing the survey design and the file log
describes the data recorded during a survey. A folder containing files belonging to a survey
is named a project folder. When a file is opened from a project folder, SonarX register the
folder name so that most operations are focused on this folder. The active folder is named
the working folder.

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If one wants to copy, move or delete a sonar file, and want to treat all files connected with
a dot uuu file, the file manager located in the file menu can be applied. See section File
manager in chapter 3.

Files in a sonar project

A file name consists of a name identifying the file and a file extension identifying the file
type. SonarX uses the following files.

Sonar source files to be converted

Extension Description
*.raw Sample data file from Simrad's EK60, EY60, ES60, EA400 or SED
telegram file from HTI
*.DGx Telegram file from Simrad's EY500 or EK500 (x indicates the year).
*.DT4 Sample data from BioSonics echo sounders
*.DAT Sample data from IOS echo sounders
Table 1. Source files used by the converter.

Files types used by the system

See also section Files produced by the converter in chapter 5 Converter.
File type Explanation

*.uuu Converted sonar files containing parameters, Amp echogram and SED
echogram.
*.nav Optional: Generated if the source file contained navigation data or
geographical position telegrams. (GL).
*.phase Sonar5 only. Optional. The converter can extract phase information from
the source file. This information can later be studied or applied by the
internal single echo detector and Crossfilter detector.
*.time The time file contains the exact timing for each ping. SonarX read this
file if available and use it whenever accurate timing is important. If not
available and for routines where speed is more important than accuracy,
time is found from the files start time and the average ping interval.
*.bottom Bottom file. If the source file contains depth telegrams the bottom file
will be produced. The bottom file can also be produced by the bottom
detector found in the Analysis = Pre-analysis menu.
*.RangeCorr If a file has been range corrected e.g. with the flat bottom command, a
file containing the range corrections for each individual ping is created
This file needed to find back to the correct range for individual samples
and detections.
*.Event File produced by the event handler or Vessel log system located in the
Survey menu.
*.txt Text file containing a text description of the sonar file. From available
information the converter generates a text file for each sonar file.
*.jpg Digital photo / image in jpg format
*.bmp Digital photo / image in bitmap format

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Table 2. Files used by the system.

Control files
SonarX.cfg Configuration files storing the program set-up. The file controls most
settings from window positions and sizes to the system parameters.
The default cfg file is located in the program folder. It is updated each
time the program is closed. The operator can freely store and load set-
ups with other file names for later use. This is done from the main menu
File=Setup
Survey.des This file stores the survey design. It is generated when the operator press
the save button in advanced file open dialogs survey design panel. The
file provides a link between transects, reference points and the map. It is
only need when a map is applied. (See the advanced file open dialog
described in chapter 3)
Survey.flg This file contains the survey log. Each project folder can contain one
default survey log. The survey log is stored in plain text describing the
files to be converted, individual parameter settings, and important events
that occurred during the recording. When opening a project folder the
converter will automatically search for this file and present it in the file-
page. The file is generated when the operator presses the save button on
the converter dialogs file-page.
Survey.srv Initial parameter file. Each project folder can contain one default
parameter file. The file is generated when the operator edits the initial
parameter setting by pressing the Initial parameter button on the
converter's file-page.
Table 3. Control files.

Telegrams
Sonar files recorded by Simrad's EY500 and EK500 operate with telegrams. The different
telegrams contain different information. To get optimal use of SonarX, it is important to
know what telegrams to record in the field. SonarX uses the following telegrams from
these echosounders.

Annotation Text messages givven from the keyboard during the recording. SonarX
extracts the messages and present them in the advanced file open menu
and in the advanced parameter dialog.
Depth D Telegram containing the detected bottom line. SonarX will
automatically extract the bottom line from the D telegram.
Echo Q This telegram contains the Amplitude echogram. SonarX can extract
the Amp echogram from the Echo telegrams.
Navigation GL The transects seen in the advanced file open dialog is extracted from the
GL telegrams.
Parameter enter PE Telegram containing parameter information. SonarX can extract the
parameters and apply them in the conversion.
Sample angle B Sample angle data telegram containing phase information. If both B and
W telegrams are available SonarX can generate an SED echogram from
these telegrams.

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Sample power W Sample power data telegram containing echo power information.
SonarX can generate am Amp echogram from the Sample power
telegram.
Trace E This telegram contain the single echo detections. SonarX can generate
the SED echogram from this telegram.
Table 4. Telegrams used by SonarX.

Two different Co-ordinate systems

Seen from the transducer, an object's position can be described by the measured angles and
range or by a Cartesian co-ordinate system. Using ship terminology, the angles are
described as Athwart ship (Ath), and Along ship (Alo). These angles are always measured
in degrees. When referring to the Cartesian co-ordinate system, x, y and z replaces the Ath,
Alo and Range axis. The units are meters. When the transducer is placed horizontally in a
river, Ath or x will point along the horizontal axis, and Alo or y will point in the vertical
axis direction. R measures the distance from the transducer. Z measures R's distance
component along the acoustic axis.

Opening files
Converted sonar files can be opened in the following ways.

 By a conventional file open dialog presenting the file names only

 By an advanced file open dialog presenting additional information from each file or
presenting a graphical view of the transects
 By a reopen dialog
 By the Quick file change functions

All the file open dialogs and file change functions are activated from the file menu. In
addition, the advanced file open dialog can be activated from the Survey menu. If no
echogram has been opened, simply clicking the echogram window can activate the
conventional file open menu.

Standard file open dialog

The standard file open dialog looks similar to the example in Figure 6. Variation may
occur depending on selected language and installed components in the computer that runs
the program. Clicking a filename and pressing the open button (here Norwegian "Åpne")
will open a file. Pressing the delete key will delete the file. By the top row buttons one can
generate new folders or change the appearance of the dialog. Right click with the mouse in
the dialog will give a list of options. Refer to a Window manual for more information
about this dialog. Note that this dialog can more than just opening a file. Copying deleting,
moving and creation files and folders are possible. This is properties provided by Windows
and not by SonarX.

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Figure 6. Standard file open dialog.

Advanced file open dialog

The advanced file open dialog has two tabulated pages, one showing the existing files by
plots of the transects relative to digital maps, and another page showing each file as a text
line with the file name together with stored information such as transect, timing, notes and
photos. The advanced file open dialog is described in chapter 03_Advanced file open
dialog.

Reopen dialog
This dialog contains the last opened files and folders. Clicking a line in the file list will
open the file. Clicking a line in the folder list will activate the file open dialog in that
folder.

Working with multiple files and Quick file change functions

More than one file can be selected at a time from the file open dialogs. Selecting multiple
files enables the quick file change, auto file change and multiple file operation features. As
an example, file number 1, 3 and 6 can be selected. The files are noted in the internal quick
file change list and the first file will be opened. Pressing Alt+N will open the next file
which is number 3 in the working folder. Repressing Alt+N will open file number 6.
Analysis processes like biomass estimation, tracking and bottom detection may be started
for all selected files and not only for one and one file.

In complex situations with multiple frequencies and many processing levels it may be
helpful to think of the files as organized in a 3D matrix with time in the x-direction,
channels or frequencies in the y-direction and processing levels in the z-direction. Using
the Quick file change short keys Alt+N, P to jump in time, the Alt+1,2,3,4.. to jump in
level and the Ctrl+1,2,3,4 to jump in frequency smooth the work.

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Navigation, GPS, UTM and NMEA

SonarX use GPS information to connect boat position and speed to the echogram. GPS
signals are used for all analysis kinds based on positions or sailed distance. GPS signal
enable the system to estimate exact position of tracked fish in GIS format and to always
present the position of pings and velocity of the boat.
Most echo sounders can store navigation information from a GPS during the
survey. This information is stored among the other echo sounder information. The
information contains a time stamp and a position description. SonarX extracts this
information and write it to a separate file with the same name as the echogram file, but
with .NAV in the extension. This file enables SonarX to present the transects in the Survey
and file open menus, to let the operator open an echogram at a geographical position, to
present where each ping was recorded, to calculate the sailed distance for an analysis
segment etc. GPS formats currently implemented in SonarX are: GPGLL, GPRMC,
GPGGA, INGLL, INRMC, INGGA. In situations where more than one string is available
SonarX will extract the one with the highes position resolution.

6048.44,N,01058.94,E
$GPGLL,5133.199,N,00346.126,E,213157,A*28
$GPRMC,213155, A, 5133.199,N,00346.124,E,2.7,68.1,270902,1.7,W*54
$GPGGA,213155,5133.199,N,00346.124,E, 1,10,0.84,-8,M,,,,*15

Where GLL = Geographical latitude, longitude and time, RMC= Recommended minimum
specific GPS/Transit data, and $GGA=Global positioning fix data.

Unitary Transversal Mercator system (UTM)

SonarX read and operate on GPS signal denoted in the longitude and latitude system.
However, for GIS compatibility Global UTM has been implemented as an option in the
most important export routines involving geographical positioning. During export, the
system will present options for positioning systems, decimal separator and preferred
number of decimals. To see this, try for example the Echogram=>Export=>Bottom menu.
Importing or modifying GPS
Missing or erroneous GPS positions can be edited or replaced with the menu:

 File => Open advanced => Import=>Import or modify GPS

The menu opens the Import GPS dialog. The dialog contains tools for selection of target
files and an editor for editing GPS positions. To modify existing positions, use the Extract
from target file button to extract the GPS signal, edit the extracted positions and press the
insert button. To apply a new GPS signal write the positions in the editor and press the
insert button. The contents of the Editor can be saved or loaded from text files to enable
editing or creation of GPS signals with alternative tools such as excel.

Use the Import dialogs Help button for more information.

Exporting Bathymetric data and with GPS
Bathymetric data with GPS, Bottom , time and ping can be exported through the Export
menu located in the

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3. Echogram => Export => Bathymetric data

4. File => Open advanced => Export=>Bathymetric data

1 exorts data from the currently presented echogram while 2 let the operator slect a
number of echogram files to export from.

Navigation error handling

The text from the GPS may contain errors such as missing numbers, commas, dots and so
on. Errors may occur due to long cables, week GPS battery, or damaged GPS. SonarX tests
the text sent by the GPS by checking for missing characters and suspicious positions. If a
character is missing or if the position jumps more than 2 NM from the previous position,
the registration is discarded. Discarded text / telegrams are listed in the converters log.
See also the section Trouble shooting in chapter 3.

Problem with GPS positions in fish baskets.

(Sonar5-Pro only)
I don’t see the correct GPS signal in my fish baskets- what to do?
Tracked targets can show both the ship and the target positions. For this it is important that
the Utilities=>Parameters=>Application page is set up correct. For example if the
application is set to fixed, then the positions presented in the fish basket will be taken from
the coordinates noted down for the base platform and not from the variable GPS signal. It
is then up to the operator to note the position of the base platform correct in the application
page. If one change settings in the application page after having tracked targets, one will
need to update the fish baskets as well.

a) Open Utilities=>Parameters=>Application page, correct settings, and press apply

b) Open your fish basket and select the top menu: Feature_Library. There you press
the Update Basket button located just above the feature list.

Parameters
There are two sets of parameters. They are:
a) Sonar parameters describing the recorded echograms.
b) System parameters controlling the program's behavior (Sonar5).

a) Sonar parameters
Sonar parameters are numbers and text related to each recorded sonar file. Some are
important for calculations while others provide information.

When a sonar file is recorded in the field, the operator sets calibration parameters, single
echo detection parameters, and environmental parameters such as sound speed and
absorption coefficient. Unfortunately, not all of these parameters are stored in the recorded
sonar file. As an example Simrad's EY500 / EK500 only stores the applied parameters if

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the operator turns on the parameter enter telegram and manually enter or request all the
important parameters during the recording.

Various tools and methods have been implemented in SonarX to help the operator dealing
with the parameters. Colors are applied to indicate the source and importance of a
parameter. An initial parameter dialog can supply parameter missing in the echosounder or
be set to overrun erroneous parameters such as sound speed and alpha. Individual
parameters for different source files can also be set up.

The converter dialog's second page has tools for writing a file log. The log can describe
parameters for a set of files or for individual files. See chapter: 5-Converter

The parameter dialog gives access to all available parameters. In addition to the
calibration and single echo detection parameters, parameters such as application
description, transducer placement and survey information are defined. See section:
Parameter dialog in chapter 10 Sonar parameters.

b) System parameters
System parameters are numbers and text related to the program. The parameters are stored
in the programs configuration file named SonarX.cfg. Parameters and tools for fish size
regression, catch statistics and species selection are found here. See chapter 11
System_parameters.

Note that Sonar4 do not need system parameters. The system parameter dialog is therefore
not available in Sonar4.

Exporting data
Data can either be exported through clip board or through files. Most dialogs and windows
have an export menu, a copy to clip board menu, or buttons named Export or Copy to clip
board. Different formats may be available in these menus. The Echogram window and the
advanced file open dialog can for example export bitmap pictures as well as numerical data
prepared for spreadsheets like Excel. In earlier versions of SonarX, Copy to clip board was
the common way to export data. In ver. 596 we started to exchange the Copy to clip board
methods with Export methods. The operator will be asked where to export the data to after
having selected one of the export options. If clip board is selected, the exported data will
end up in the clip board from where it easily can be transferred to other programs like
Excel or Word. Using the Edit => Paste menu or pressing Ctrl + V in these programs will
paste the data into these programs. If file is selected, the operator will be asked for a file
name. See for example the export menus in
1. Chapter 3 Advanced file open dialog to export file, survey, transects, GPS and Bottom
information.
2. Chapter 6 Echogram window to export echogram samples, echogram picture, GPS, and
bottom.
3. Chapter 8 Biomass window to export biomass analysis results.

1 and 2 are frequently used e.g. for GIS and bathymetric work.

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Printing echograms
Preparation
The printer routine will copy the entire echogram window and stretch it to the available
paper size and orientation. Hence, it is important to adjust the echogram according to what
one want to print.

 Adjust the size of the echogram window. A small window will result in many pages
with a high degree of stretching.
 Select range and degree of zooming or compression.
 Select whether to display the Amp or SED echogram.
 Select echogram threshold.
 Select whether to display the range, ping and color bars and their colors.
Note
The printer will print everything within the frames of the echogram window. Placing a
dialog so that it covers parts of the echogram will result in a printout where the echogram
is covered with the dialog as it appeared on the screen. This is correct and can be used to
mix a print of an echogram with additional information from other windows such as the
echogram information window or the position diagram

The main menu

Figure 7. The main menu in SonarX.

The main menu is a pull down menu located at the top of the program as seen from the
figure above. The items are described below.

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File menu

Figure 8. Items in the file menu

The file menu contains tools for handling sonar files. This includes opening, closing,
converting, printing, re-sampling, and configuration set-up.

Items Explanation
Open Activates a standard windows open dialog.
Open advanced Activates the advanced file open dialog described in chapter 3.
Reopen Activates a dialog showing the latest used files and folders.
Close This menu closes a sonar file. If a sonar file displayed in the
echogram window is to be deleted, moved or copied by the file open
dialog, it must first be closed. The file open dialogs close the file
only when a new file are opened.
Select all files... Adds all sonar files in the working folder to the internal quick file
change list. This list enables the quick file change and auto file
change functions.
Selecting a subset of files for the list can be done in the file open
dialogs.
Quick file change This is a sub menu with items for opening original or processed files
or the first, the next, the previous and the last file listed in the
internal quick file change list. See the section Working with multiple
files in this chapter.
Convert Activates the converter dialog. See chapter 05 Converter
Print Prints the echogram on a bitmap color printer. See Printing
echograms.
Set-up This is a sub-menu with menu items for saving and loading the
program configuration file. Different configurations can be saved in
different files for later use.
Explore working Opens windows explorer to present the files in the folder where you

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folder currently are working..

File manager Use this dialog to copy, move delete or rename sonar files or folders.
Selecting a sonar file will detect all files related to that file such as
picture, text, bottom and phase files. Copying or moving will then
ensure that all needed files are handled. See section "File manager"
in chapter 3.
Resample This menu opens a dialog that can resample selected files into new
file with shorter range and changed base threshold. See section
Resampling in chapter 3.
Merge This menu opens a dialog that enables merging of multiple
converted files into one new file. See section Merging in chapter 3.
See also merging files in chapter 5
Exit Saves the default set-up file (SonarX.cfg) and terminate the
program.
Table 5. File open menu.

Echogram menu
The echogram menu activates the Echogram window's popup menu. See the section
Echogram popup menu in chapter 06 Echogram window for the description of this menu.

Analysis menu

Figure 9. Analysis menu.

This menu controls the analysis. It has sub-menus for pre-analysis, for setting up the
analysis method, selecting the region to be analyzed and for executing the analysis of
selected regions. Pre-analysis contains methods such as noise filtering, bottom detection,
single echo detections and Crossfilter detection. The setup menu prepares the program for
methods such as biomass, estimation, tracking and data insight. The Software Guided
Analysis (SGA) guides the operator through the analysis. See chapter chapter 4 for more
information.

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Utility menu

Figure 10. Utility menu

Parameters Activates sonar parameter dialog at the page selected in the

parameters sub menu. See the section sonar parameter dialog
in chapter 10-Sonar parameters.
System Opens the system configuration dialog at the selected page.
See chapter 11 System parameters.
Editors => Working notes Opens an editor related to the working folder and intended for
survey notes, Files are stored in the active working folder.
Editors => General notes General notes meant for general comments concerning the
system or all surveys. Files are stored in the systems program
folder.
Editors => Calendar The calendar is meant to assist in planning
Tools => Sound propagation Opens the dialog controlling the tracing.
and ray tracing
Tools => File statistics Display information such as number of pings and number of
single echo detections. File statistics can also be found in the
advanced sonar parameter dialog's echogram page and the fish
basket dialog's option menu. (Chapter 10 and 14)
Tools => Screen grabber Screen grabber with timer and burst options
Tools => Calibration Opens a calibration dialog for simple calibration. If a standard
target has been recorded in the center of the beam, Correct gain
can be found with this dialog by tracking parts of the recorded
echoes.
Tools => Time adjustment Changes the timing of an echogram forward or backword
Tools => Pen detector Special detector for detecting the net in a fish pen
Tools => Sound proagation Useful for predicting the soundspeed and alpha as functions of
and ray tracing depth in vertical applications, and to check the refrection and
reflection of the sound beam in horizontal applications
Tools => SED range Tools for adjusting range of the single echo detections.
adjustments Originally implemented to correct mismatch between
transducer depth and surface depth in the amp and SED
echogram.
Tools => EY500 and EK500 Simrads 40 log amp echogram recorded with Qtelegrams have
40 log echo telegram offaxixcompensated samples at places where single fish has
correction. been detected. This makes the echogram useless for echo
integrations. The algorithm removes the compensation in order

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to maker the echogram useful for echointegration.

Tools => Reinstall Licence
driver
Programs
Under construction
Table 6. Utility menu items
Let you move sonar5 to another PC without having to run the
installation CD
Here you find and can start some additinal programs such as
the Site calculator, Beam calculator and the image browser
New methods are located her such as
Seabed classification.

Stop menu
Pressing the stop menu will break a time consuming analysis as soon as possible.

Survey menu

Figure 11. Survey menu

Overview plot transects graphically and indicates with graphical marks where additional
data has been recorded. The map can be displayed simultaneously with the echogram.
Clicking at a point on a transect in the map will show that part of the transect in the
echograms. If one move around in the echogram, the map will indicate what the echogram
cover by plotting that part of the transect with red color. See Chapter 21 section Survey
overview for more information about the survey overview.

Vessel log and event handler is a system that enables marks with associated comments to
be placed in the echograms. Marks can be vertical lines places e.g. every nautical miles
starting with the first ping in the first file, or lines, boxes and free hand drawings pointing
out special events. The system can jump to and from these marks. Marks can be generated
manually, automatically or be generated from notes in a text file. See Chapter 21 for more
information about events and vessel log.
Show transects
Open will open the survey map dialog showing transects graphically. The dialog can also
open additional data files such as hydrographic data and trawling, and link the files to the
transect lines. Navigation data from a GPS must have been recorded together with the
echogram for transects to be seen in this dialog. (See the section Navigation, GPS and
NMEA in this chapter)
Edit map
Opens the advanced file open dialog at the transect design page in edit transects mode.
This enables applying maps and placing reference points.
See chapter 03_Advanced file open dialog for more information.

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Vessel log generator

This menu item opens the event handler at the Generate new vessel log page. The
generator can generate distance or time based marks in the echogram. Each mark is an
event which can be browsed by the event browser and edited by the Event editor. See the
Vessel log section in chapter 21
Event Editor
This menu item opens the event handler at the Edit event page. See the Event editor section
in chapter 21
Event browser
This menu item opens the event handler at the Browse event page. See the Event browser
section in chapter 21

Internet menu

Figure 12. Internet menu with a list of important links. Clicking a link will open the
installed internet browser which will tempt to connect to the indicated link.

Help menu
This menu has three items, main, xxxx and about. Main opens the main file containing
links to all the other help files while About opens the about dialog. The menu item xxxx
will take on different names depending on which of SonarX's child windows that are active
at the moment the menu is accessed. E.g. if the echogram window is active when the help
menu is accessed, xxxx will be Echogram and the echogram windows help file will be
opened if this menu is selected. Activating the position diagram window before accessing
the help menu will show the position diagram windows help file and so on.

TVG and sonar equations

TVG determines how much the echo intensity should be compensated due to increasing
range. Sonar equation is the model applied to interpret the returned echo intensity. Two
common equations or models are frequently applied. They are the point source model used
to interpret single targets and the volume reverberation model used for echo integration of
fish schools. It is common to associate TVG with the sonar equation. 20 log R is associated
with the volume reverberation model, while 40 log R is associated with the point spread
model. This is only correct when spherical spreading is assumed.
The applied TVG is displayed in the
 Caption of the Amp echogram.
 Sonar parameter dialog's echogram information page

See the section TVG and sonar equation in chapter 10 Sonar parameter dialog for more
information.
What TVG to select is described in chapter 6, in the What TVG to select section.

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Changing TVG
SonarX can change sonar equation and TVG after the file has been converted. This is done
from the main echogram menu's TVG menu. The TVG menu is a submenu with three
items. See the TVG menu section in chapter 6 for more information. In SonarX’s image
analysis commands, a separate command for changing TVG has been defined (See the
ChangeSonarEQ command in chapter 15 command section.) (not available in Sonar4)

Understanding windows
Microsoft 's Window is a family of operating systems such as Win98, WinNT, Win2000,
WinME, and WinXP. In a Window based PC, a user program are called an application.
SonarX is an application. Each application may consist of one or more windows. There are
different kind of windows such as the main window also called a parent window, sub-
windows within the parent window and dialogs that appear and disappear during the
applications lifetime. The inside of a window can be filled up with components such as
buttons, panels, text-boxes, images, etc. components may be separated by splitters.

Parent and children windows

A multiple window application is called a parent /child application. All the windows
located within the parent window are called child windows. Child windows can be born,
activated, deactivated, resized, moved and killed by the parent. Pointing the mouse at the
child window's top and pressing the left mouse button activates the child.

Pull-down and popup menus

A window can have two types of menus, pull-down and pop-up menus. Pull-down menus
are always visible at the top of the window while the pop-up menus have to be activated by
pressing the right mouse button within a window. Each child window can have its own
pop-up menu. It is important to remember that it is the popup menu from the window
under the mouse pointer that will pop up when the left button is pressed.

Activating a window
Pointing the mouse to a windows caption and pressing the left mouse button activates the
window. Caption is the top panel of a window. Only one window can be active at a time.
The color of the window's caption indicates whether a window is active or not. By default,
dark blue indicates an active window while gray indicates an inactive window. It is
important to be aware of this, especially when the keyboard commands are used. As an
example, pressing the F1-key when the echogram window is active will open the echogram
help file. If another window is active, this window's help file will appear and not the
echogram windows help file.

Figure 13. Example of an actived (left) and a deactived window (right) The differece is the
color in the top line called the windows caption.

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Splitter
A splitter component is a horizontal or vertical thin bar separating components within a
dialog or window. When moving the mouse slowly from one component to another the
mouse cursor will change into two parallel lines when passing a splitter. When the parallel
lines occur, one can press the mouse button and move the splitter. This will change the size
of the surrounding components. This is convenient for example if one want to enlarge a
picture or to see more of the text in a list. Splitters are applied many places in the program.
Examples are found in the converter, in the advanced open dialog, and in the advanced
sonar parameter dialog.

Demonstration files
SonarX’s installation CD contains demonstration files. Different scientists have
contributed. Various kinds of equipment have recorded the files in different environments.
We have divided the files into groups such as rivers, lakes, oceans, experiments, noise, etc.
The files are intended for training and for studying echo phenomena.

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Main menu

ABOUT .....................................................................................................................................................................49
OPEN BY FILE INFORMATION ....................................................................................................................................50
File info list ........................................................................................................................................................50
Changing the information stored in the file descriptor ......................................................................................50
File control panel ...............................................................................................................................................51
Photo ..................................................................................................................................................................51
Text.....................................................................................................................................................................52
OPEN BY TRANSECTS ...............................................................................................................................................52
Transect info list-box .........................................................................................................................................53
Mouse pointing at...............................................................................................................................................53
Transect control panel .......................................................................................................................................53
Open and close buttons ......................................................................................................................................53
Trouble shooting ................................................................................................................................................53
SURVEY DESIGN .......................................................................................................................................................54
Maps...................................................................................................................................................................54
Reference points .................................................................................................................................................54
THE TOP MENU.........................................................................................................................................................54
File menu ...........................................................................................................................................................55
Import menu .......................................................................................................................................................55
Export menu .......................................................................................................................................................55
Option menu .......................................................................................................................................................27
Refresh ...............................................................................................................................................................28
Help ....................................................................................................................................................................29
FILE MANAGER ........................................................................................................................................................29
RESAMPLING ...........................................................................................................................................................30
MERGING .................................................................................................................................................................31

About
The advanced file open dialog has two pages, one page displaying the converted sonar files
by name, and a second page displaying the files by drawing transects. The file page opens
each sonar-file found in a folder and displays not only the filename, but also information
found in each file. Pointing at a line with the mouse will bring up the description file and
photo connected with that particular file.

The transect-page opens all navigation (*.nav)) files found in the folder. If the folder has
been provided with a survey design, transects will be displayed in a map.

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Open by file information

A G

B E

D
C

Figure 14. Advanced file open dialog showing the file info page. A) pull-down menu, B)
file info list, C) photo file, D) text file, E) file control panel, F) drive and folder selector,
G) Open and close buttons, H) Splitters

File info list

The file info list (B in Figure 14) displays the converted sonar filenames found in the
selected folder. A description record is stored in within each converted sonar-file. The
record contains information such as survey, transect operator, picture filename and text
filename. When presenting the file names, this additional information is extracted and
presented as well. The file information control panel (E) controls what information to be
displayed. Pointing at a line and clicking once with the left mouse button presents the
picture and text file connected with that particular file. The file info list is sorted on the
first presented column which can be the filename but also timing, number of pings etc.

Changing the information stored in the file descriptor

 Select one or a set of files and press the Open selected button.
 Open the parameter dialog at the description page.
 Write the changes and press the parameter dialogs update menu.
Press Ctrl-N to advance to the next selected file.

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File control panel

The information control panel (E in
Figure 14) controls the information to be presented in the file list.
Whenever changes are made , a read update button will appear on the top. This has to be
pressed to see the changes in the file list.

Tabulator
The tabulator boxes decides how many characters to present form each label. Here the
filename will be presented with max 35 characters.
Number of ping checkbox
If checked, the number of ping within each file will be displayed
Date time checkbox
If checked, the date and time of each recording is displayed
Survey info checkbox
If checked, the text string describing the survey will be displayed.
Transect info checkbox
If checked, the text string describing each transects will be displayed.
Diurnal coverage checkbox
If checked, the percent of the day covered by each recording will be presented. A summery
of total coverage will be displayed at the end of the file list.
Channel filter
Many echo sounder systems can store data from different transducers in the same file. To
ease processing speed SonarX split these files during conversion, and give the individual
filenames with different channel numbers. The triangle to the right let you se all or
specific cahnnels in the file list.
Processed Level filter
Some operations can generate new sonar files like the change TVG function. The new file
will have the same filename, but a letter Q added to the extension to indicate that the file is
a processed sonar file. By default, the file filter accepts all converted sonar files but
clicking the triangle to the right let the operator select special levels.

Same Q number
The Q number indicate the processing level of an echogram file. A multi channel file may
contain echograms that exist in different processing levels. The selector eneable the
operator to tell what level the system should look for at the other channels when opening a
channel.

Photo
Each converted sonar file can contain a file name pointing to a digital picture. The picture
must be stored in jpg format and located in the same folder as the sonar file, its super
folder or in the same folder as the SonarX program. Pointing at a line in the file list will
present the picture referred to in that file. A digital camera, a scanned picture or a drawing
from a program like paint can be used to remind the operator about the recording situation
or to identify the different files. The picture name was originally set when the sonar file

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was converted (chapter 5). It can be changed in the parameter dialog (chapter 10).

Text
Each converted sonar file can contain a file name pointing to a text file. The text file must
be stored in plain text and located in the same folder as the sonar file, its super folder or in
the same folder as the SonarX program. Pointing at a line in the file list will present the
text file referred to in that file. The text file is generated when the converter (chapter 5)
reads the information in the survey log (survey.flg file). By default, a new text file is
generated automatically for each converted sonar file. The text file name can be changed in
the parameter dialog (chapter 10).

Open by transects
See also the survey menu
I
A J
(

C
H
G

E F

Figure 15. Advanced file open dialogs transect page with the design panel activated. A)
Pull down menu, B) Map, C) Reference points, D) Transect, E) Transect info listbox, F)
Mouse position information, G) Drive and folder selectors, H) Transect control panel, I)
Open and cancel buttons, J) Splitters

If GPS information has been recorded, the boat positions will be plotted as lines.
Double clicking with the mouse at a point along the track will open the recorded echogram
at the selected time and position. (See also transect info)

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Transect info list-box

If the mouse is pointed at a position on a transect and the left mouse button clicked once,
the time when the boat passed that point and the name of the recorded file will be
displayed in the transect info list box (E in Figure 15).

Mouse pointing at
When the mouse is moved around in the transect panel, the "Mouse pointing at" panel will
translate the mouse positions into geographical positions. If a map has been applied, the
positions will be correct according to the map provided that the reference points are
positioned correct.

Transect control panel

This panel has the following check boxes
Show survey design
Uncheck this to force the program to always open the echograms from ping 1.
Open at selected time
Uncheck this to force the program to always open the echograms from ping 1.
Drive and folder selectors
Sonar recordings from different surveys should be placed in different folders and
directories.
The pull-down file menu can be used to create or remove folders and to move, copy or
delete sonar files. The Drive and folder selector displays the available folders on the
computer and let you change from one folder to another.

Open and close buttons

Open selected button
Opens the file selected by the mouse in the file list. If more than one file is selected, the
first will be opened while the remaining of the selected files will be added to the quick file
change list. The idea with the quick file change list is that the operator can select a set of
files to be analyzed as an alternative to go back to the file open dialog each time. See the
paragraph: "Opening files in the chapter "Getting started" for information about the quick
file change function

Open all button

Open the first file in the file list and places all files in the quick file change list.

Close button
Close the dialog.

Trouble shooting
Why do I not see the transect lines?
a) If files from different geographical places are stored in the same folder, transects
will look like dots and not bee easy to see. Splitting the files into different folders
will solve the problem.

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b) The reference points have been set wrong. A transect is short relative to the globe
and it is easy to set the reference position so that transects will be plotted outside
the visible transect panel. Pressing the Auto scale button will solve this.
c) The transect files does not exist in the same folder as the sonar files. A transect file
has the same file name as the sonar file, but the extension is dot nav.
d) The transects looks strange. Errors may have occurred when the GPS transferred
the data to the echo sounder. SonarX versions v590 and newer have improved error
checking and the problem may be solved by reconverting the file. In newer
versions, the NMEA information can be listed in the converter log if list NMEA is
turned on in the converters option menu. This may be a help to see what has gone
wrong.

Survey design
Survey design in this context does not mean designing your fieldwork, but adding maps
and setting reference points in that map. The needed tools are located in a separate panel
located in the center of the transect page. The panel will be visible if the survey design
checkbox seen under H in Figure 15 is checked.

Maps
To display a map, a digital map must be placed in the same folder as the sonar files. The
file format must be bitmap (*.bmp), and the file name must be noted in the survey panels
map edit box. The map name is stored together with the reference points in the file named
Survey.des when the save design button is pressed. Maps and transects are linked together
by reference points.

Reference points
There are two reference points, one rectangular and one circular. Placing them at two
known positions in the map ensure that transects will be plotted correct in the map.
How to set the reference points correct
If no map is available, pressing the auto-scale button is sufficient. Otherwise:
1) Find two reference positions on the map and fill out the names and the geographical
positions in the Survey design panel for each reference point.
2) Point at the reference point symbol in the map, press the left mouse button down and
move the mouse to the correct position in the map. Drop it by dropping the mouse
button.

Cities, islands, mountains, rivers outlets etc. can be used as reference points.
Note! The two reference points must not be positioned on the same latitude or longitude.

The top menu

The top menu contains the following items;- File, Edit, Option and Help.

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File menu
Open
Activates a traditional file open dialog.
Reopen
Displays a list of previous opened folders. Clicking a line here will bring the program to
this folder if the folder exists.
Convert
Opens the converter.
File manager
Use this manager to Move, copy, delete, rename, remove write protection and create new
folders. See File manager

Merge and resample

Opens the dialog that enables merging files together or re-sampling them to other lengths
ranges, ping rate and so on.

Import menu
The import menu enables import of artificial GPS data. If the GPS mail functioned during
the survey or position information was not stored through the echosounder, this menu may
be a help. Selecting Import GPS will open a dialog. The help button in this dialog provides
the necessary information.

Export menu
The export menu has items for exporting data to clip board or to file. The operator will be
asked where to export the data to after having selected one of the export options. If clip
board is selected, the exported data will end up in the clip board from where it easily can
be transferred to other programs like Excel or Word. Use the Edit paste menu or press Ctrl
+ V will paste the data into these programs. If file is selected the operator will be asked for
a file name. The following options are available in the export menu.
File information
Export the file names and text seen in the advanced file open dialogs file page. The
information can be pasted into programs like Word and Excel by activating these programs
and pressing their short-key Ctrl + V.
Diurnal coverage
This menu exports how many percent of each day that is covered by recordings. This is
useful for fish counting surveys and similar work where percent diurnal coverage is of
importance.
Map with transect as bitmap
Copy a graphical picture to clip board. The picture will show the available map and
transects.
Bathymetric data
This method produces a table containing time, ping GPS and bottom depth.

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Option menu
Sort on
The file list can be sorted on all the information available to the file list selected in the right
dialogs right panel. By default files are sorted by filename, but can be sorted on File
number, Number of pings, Date and time, survey info or transect information.
Renumber selected transects
Each file is automatically given a file number in the conversion process. The number is
displayed behind the filename in the advanced file open dialog. It can be convenient as an
alternative reference to the file instead of the actual file name. Discussing file number 10 is
easier than discussing filename 03112210. The menu let the operator renumber the file
numbers assigned during conversion. Select the files to be renumbered in the file list.
Then select this menu item. A dialog will guide the renumbering.

Refresh
Some operations generate new files. If the advanced file open dialog is accessed after new
files have been generated, dialog may need to be refreshed to show them. Some operations
place the new files first in the list with a special text stating that they are new files.
Pressing refresh will sort and list these files in the ordinary way.

Help
Opens this chapter.

File manager

Figure 16. The file manager is opened from the advanced file open dialogs File menu.

The file manager can be opened from the Advanced open dialogs file menu, from
SonarX’s main file menu and by double clicking in the converters page 3, lower left file
list. The file manager has been implemented to handle survey folders and files in a survey.
When opened, the manager will be in default mode. In default mode, converted files will

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be listed in the source file list box. Files selected with the mouse in this list will be reported
in the center report memo together with all files connected with the selected files.
Examples are bottom, navigation, text, picture, and event files. If a related file is found in
another folder the location will be included in the list. Listed files can then be moved,
copied, deleted and so on. Common files used by other files will be protected from
deletion, and with moving operation they will be copied instead. In the remaining
operation modes, the dialog works like an ordinary file and folder manager. No search will
be performed and the selected files or folders containing all files from a survey can be
handled according to the selected tasks.

Resampling

Figure 17. This dialog can resample selected sonar files. Re-sample means changing
threshold range number of pings and number of samples.

Using the dialog

1. Select one or more files in the file list box seen at the left side of the dialog. The
"Select file" button above the file list box can be used to select files from a different
folder.

2. The AMP and SED parameters seen in the right side of dialog will be adjusted
according to the first selected file. After selecting files, change the parameters to the
wanted values. Note that max range and threshold only can be reduced, not increased and
that min range only can be raised.

Pressing the run button will resample the files with the new setting. The result will be
written to files with the same names as the original names, but with a suffix “R_” added to
the filename to indicate that it is a re-sampled file. Clipping out a bit of a file, reducing the
ping rate, changing thresholds, range resolution and range is possible with this dialog.

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Merging
The dialog for Mergin look similar to the resample dialog.
All selected files will be merged into one large file. This file will be given the name of the
first selected file, but with an "M_" as a suffix. The original files will not be overwritten or
changed. During merging, threshold and range can be reduced. No warning will be given if
the different files have been recorded with different parameter settings or with missing
time periods between. The new file will adopt the settings applied in the merge dialog
together with and the parameters settings in the first selected file. The parameters in the
parameter dialog can be set manually or extracted from one of the files seen in the dialogs
file list to the left. Point and click with the mouse on the filename to extract the parameters
from.

Files pre-processed with the heave or flat bottom methods should not be merged. Merge
files first and then apply heave or flat bottom to the merged file.

Pressing the Merge button will merge all files into one new larger file. The result will be
written to a file with the same name as the first selected file, but an M will be added as a
suffix to ensure that none of the original files are overwritten and to ease finding the file in
the file open menu. The Min Max and threshold value seen in the dialogs Amp and SED
panels will be valid for the new file.

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Main menu

ANALYSIS CONTROL ................................................................................................................................................60

THE MAIN ANALYSIS MENU ......................................................................................................................................60
PRE-ANALYSIS MENU ...............................................................................................................................................61
Filters .................................................................................................................................................................61
Noise ..................................................................................................................................................................61
Target – noise separation...................................................................................................................................61
Erase Noise by hand ..........................................................................................................................................61
Passive noise subtraction ...................................................................................................................................61
Max range detection...........................................................................................................................................61
Interfering echosounder .....................................................................................................................................62
Cavitation ...........................................................................................................................................................62
Single echo detection .........................................................................................................................................62
Crossfilter detection ...........................................................................................................................................65
Bottom detector and inspector ...........................................................................................................................66
Heave correction ................................................................................................................................................73
Flat bottom echogram ........................................................................................................................................74
ES60 correction implemented ............................................................................................................................74
ANALYSIS ................................................................................................................................................................78
Setup, adding and removing analysis .................................................................................................................78
Select region to be analyzed ...............................................................................................................................81
Variable layer thickness .....................................................................................................................................82
Start analysis ......................................................................................................................................................83
ANALYSIS METHODS ................................................................................................................................................49
Tracking .............................................................................................................................................................50
Biomass estimation ............................................................................................................................................50
Macrophyte analysis ..........................................................................................................................................50
SEABED CLASSIFICATION .........................................................................................................................................51
Analysis preparation ..........................................................................................................................................51
Feature definitions .............................................................................................................................................52
Seabed feature description .................................................................................................................................52
Integrals .............................................................................................................................................................53
Secondary features .............................................................................................................................................53
Multi frequency analysis ....................................................................................................................................53
DATA INSIGHT .........................................................................................................................................................53
3D-Echogram window .......................................................................................................................................53
DIDSON Viewer .................................................................................................................................................54
Oscilloscopes window ........................................................................................................................................54
Sample data analyzer .........................................................................................................................................54
Position window .................................................................................................................................................54
Echogram window..............................................................................................................................................55
Integram window................................................................................................................................................55
Frequency response ...........................................................................................................................................55
Track information ..............................................................................................................................................27
TS versus range and how to find the layers........................................................................................................28
TS distribution and threshold setting .................................................................................................................29
Eckmann threshold .............................................................................................................................................29
SED as a function of increasing opening angle .................................................................................................30
Display the actual beam function .......................................................................................................................31

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Analysis control
To analyze something, set up the windows dealing with the wanted kinds of analysis and
either use the mouse directly in the echogram to select what to analyze and to start the
analysis or use one of the two analysis control dialogs. See the sections Analyze control
page and Alternative analysis control dialog in chapter 7.

The main analysis menu

Figure 18. Analysis menu

Echosounder data analysis can be divided into four main categories, pre-analysis,
analysis, interpretation and data
1. Pre-analysis are processes such as noise filtering, single echo detection and bottom
detection.
2. Analysis includes Tracking, Biomass, and Macrophyte estimations.
3. Interpretation deals with the meaning of the output from the analysis.
4. Data insight also referred as echogram scrutinizing, means looking into the data.
Being able to look into the data can assist methods in each of the other categories.
Insight is also important for experimental work such as studies of sound
propagation, beam behavior, near / far field experiments etc.

About menu
This menu item opens a quick help file describing the basic use of the analysis menu
Setup
This menu is relatively new and was implemented to take over for the Analysis method
where one have to enter quite many sub menus before getting to what one wants. Selecting
setup opens a tabulated dialog where the most common setup templates are available with
buttons on the first page. More options are available on other pages, and the dialog has also
room for comments about what the different setups will provide. We have however left the
older analysis menus intact because many operators prefer them.

SGA (Software Guided Analysis). This will lead the operator through a check list, and for
each step, set up the system for that particular task, and give recommendations and
background theory. Current SGA cover biomass estimation for vertical mobile surveying.

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Pre-analysis menu
Before one can analyze the data with processes such as tracking or biomass estimation, it is
necessary to separate single fish echoes from schools. It may also be necessary to remove
noise, to detect a bottom line, and to correct for heave.

Filters
Selecting Analysis =Pre-analysis =Filters opens the filter template dialog. This dialog
can be used to remove noise from the Amp echogram. The filter dialog is described in
chapter 15 Image analysis.

Noise
Noise is everything one does not want and the technique to apply depends on the nature of
what you do not like. It can be single echo detections from fluctuations in the background
or from debris in a river, electric interference or targets that disturb the analysis. This
menu contains the following sub menus for handling noise.

Target – noise separation

This menu opens a detector designed to separate echoes from wanted and unwanted
targets. A mask can be made and applied to other channels or frequencies. Detected targets
can accepted while the surrounding echoes can be removed or vice versa. The method can
be set up to use the Crossfilter detector or a fixed upper and lower threshold. The template
is described in chapter 19’s section Target-noise separation

Noise can also be removed with the manual noise erasing tools described in chapter 7’s
"Layer, bottom and noise" section, by filtering and by tracking unwanted targets and
stating that these targets or the layer where the targets are found should be erased.

Erase Noise by hand

Opens the manual noise tools located in echograms control dialog. See also erase unwanted
echoes or noise in chapter 6 echogram.

Passive noise subtraction

Opens a dialog that enables the operator to detect and remove passive noise from
echograms. Passive noise can be automatically detected and removed, or passive noise can
be studied in passive or active recorded files and then subtracted from the echograms. See
Passive noise in chapter 16 Oscilloscope window. The dialog uses the “PassiveNoise”
command described in chapter 15.

Max range detection

This menu opens a detector designed to detect an objective maximum range based in files
where the noise level increases with range and fluctuates with time. Fixed mobile or
horizontal applications where the beam is aligned close to the surface or bottom are typical
examples when this method may be needed. The method detects the range for each ping
where the noise exceeds a selected level. This line normally thought of as the bottom line,
is then applied at the detected range. Here it will prevent analysis from being performed at

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higher ranges in the same way as when the line is applied as bottom and prevent analysis
of bottom signal.

Interfering echosounder
Opens a dialog designed to remove disturbing vertical bars in the echogram. Such bars are
often produced by other nearby acoustic tools.

Cavitation
Opens a dialog deigned to remove spikes in the echograms. Cavitation from a propeller
can produce such spikes.

Single echo detection

Single echo detection is important for tracking and biomass estimation. Single echo
detections are presented in the SED echogram and in the position diagram. SonarX can
obtain single echo detections in four ways
1) By extracting single echo detections from trace telegrams. See the section 3b) SED
echogram panel in chapter 5-Converter.
2) By applying an internal single echo detector during conversion. See the section
Applying the built-in single echo detector in chapter 5.
3) By applying the Single echo detector accessed from the Analysis=pre-analysis menu,
described in chapter 20.
4) By applying the Crossfilter detector accessed from the Analysis=pre-analysis menu,
described in chapter 19.
What is Single echo detection
If two fish enters the sound beam at the same range, the transducer will receive the echo
from the two at the same time. The echoes will interfere. If the targets are located slightly
at different ranges or with different angular positions, the echo may be elongated and may
have two peaks. The standard deviation in the phase samples may increase. The system
will not be able to determine the correct number of targets, their sizes, and positions. The
single echo detector tempts to suppress such echoes by testing the echo-pulses with the
SED-criteria. The folder Balk_Lindem / Sonar demo files/ experiments / Target
interference contains files where two standard targets slowly are moved together. Use these
files to study interference between approaching targets.

The echo length criterion

Echo length is the echo distribution in the range domain. The detection algorithm searches
for a local peak in the sampled echo signal. The algorithm trails both sides of the pulse
until it finds the first sample below 6 dB relative to the peak. The absolute echo length is
measured in numbers of samples between start and stop. The transmitted pulse length is
converted to a number of samples as well. The measured echo length is divided by the
transmitted pulse-length to obtain the relative echo length. The result is compared with the
min. and max. echo length criteria to see if the echo can be accepted or not.

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a) Peak_TS

b) PeakTS-6dB

0 1 2 3 4 5 6 7 8 9 10 1112 13
e) Pulse width
c) Pulse start=3 d) Pulse stop=10
Figure 19. Definition of a sampled echo-pulse. a) peak TS. b) A threshold is set 6 dB
below the peak TS. c) Pulse start is defined as the first sample after the threshold is passed
with raising intensity. d) Pulse stop is defined as the first pulse after the –6 dB threshold is
passed with falling intensity. e) Pulse width = Pulse stop - pulse start. ( Here 7 = 10 - 3.)

The Max. Gain Compensation criterion

Max.Gain.Comp (MGC) also called max. beam compensation defines the cross-section
width of the beam. Echoes detected outside the circle or ellipse defined by the MGC in
conjunction with the transducers opening angle will not be accepted as single echoes. The
gain compensation factor that MGC works on is calculated by the application of a Bessel
function as demonstrated in the following expression.


GC  2  3  2   2  0.18   2   2 
Eq. 1
Alo Ath
 
3dBBeamwAlo / 2 3dBBeamwAth / 2
Where GC = Gain compensation factor, Alo = mean along-ship angle, Ath = athwart-ship
angle. The 3dBBeamwAlo and the 3dBBeamwAth denote the transducer opening-angle (4
and 10 deg. respectively with the ES120 4x10 transducer).
Max. phase deviation
Warning: This parameter differs from the definition applied by Simrad in that it is
calculated from true angles in degrees and not from the echo sounders internal electrical
degrees.

Phase Deviation (PD) is calculated as the standard deviation of the angle samples within
each echo-pulse from the along-ship (Alo) and athwart-ship (Ath) domain. With a pulse-
duration of 0.3 ms, a sound frequency of 120 kHz and a sample rate of 24 kHz, 6 - 8
samples are normally found within the duration of a single echo.

sAlo 
1 N

 Alo  Aloi
N  1 i :1

2

Eq. 2
sAth 
1 N

 Ath  Athi
N  1 i :1

2

PD  Max( sAlo, sAth )

If PD  Max.PhDev then reject the echo

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N is the number of samples in the pulse. Alo and Ath refer to the along-ship and athwart-
ship axes defined for the Simrad transducer. SonarX calculate the standard deviation from
the mechanical angles.

Note that Simrad's echo sounders calculate Max. Phase dev. (MPD) based on the electrical
phase steps, and that the definition of phase steps varies between the different echosounder
models. SonarX applies MPD measured from mechanical degrees in order to have one
standard for all echo sounders. Another reason is that it is easier to present standard
deviation measured in degrees in papers and to explain it to people not familiar with the
interior of Simrad’s echo sounders.

Standard deviation measured in degrees and in phase steps can be related by applying the
scaling factor between degree, phase steps and the electric to mechanical sensitivity factor.

64
sAth ps  sAth  AngleSensi tvityAth  (Simrad 500 echo sounder series)
180
Eq. 3
120
sAth ps  sAth  AngleSensi tvityAth  (Simrad 60 echo sounder series)
180
Where sAthps = standard deviation measured in phase steps and AngleSensitivityAth =the
electric to mechanical sensitivity factor in the Athwart domain.
Conversion between SonarX and Simrad Max phase deviation parameter
The dialogs dealing with this parameter is equipped with a converter calculating what a
Max. phase dev. setting in SonarX relates to in the 60 and 500 echo sounder series. The
converter opened by clicking on the following text line in the dialogs.

* Click this line to see how Max. phase dev. = 0.3' relates to Simrads Max.phase dev. parameter.'

Clicking will open Max phase dev. converter dialog

Figure 20. Max phase dev. converter dialog converts true standard deviation into Simrads
electrical phase step deviation.

Angle sensitivity must be set correct to see the correct relation. When ever an input value

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is altered, the “Relates to” panel will be updated.

Ok button
Pressing the ok button will tempt to copy changed parameters into the parent dialog. The
attempt will be rejected for any parameter having disabled (gray) color in the parent dialog.
Cancel button: will simply close the dialog without any updating attempts
The multiple peak criterion
This criterion rejects an echo if the echo has multiple peaks. The criterion can be set to off,
medium and strong. With medium, the pulse may have multiple peaks, but the local
minimal point between the peaks must be less than 1.5 dB. When set to strong, no local
minimal point is accepted. Default value is medium. The criterion was originally
developed by T. Lindem. Simrad has included medium suppression as default in the 60 and
500 echo sounders.

Problems with traditional Single echo detectors

The most profound problems with traditional ping to ping criteria based ingle echo
detectors are
a) Erroneous detections from fluctuation in the background reverberation
b) Missing detections from fish.

This leads to erroneous tracking and biomass estimation analysis.

For biomass estimation it is more important to avoid noise based echoes than to obtain nice
tracks with few missing echoes. Strict adjustment of the criteria is essential. E.g Echo
length =[0.8..1.2], MGC=3 and PhDev=2 (EY500 phase step). Sonar files recorded with
strict SED criteria are, however, often not well suited for tracking due to ping-gaps or
missing detections in the tracks. Reducing the strictness in the parameters can help, but this
may lead to more noise based detections surrounding the tracks.
Trimming the SED-parameters can be a solution
The EY500 echo sounder can record SED echograms directly on the hard disk in real time.
This results in very small files, but has the drawback that the detection cannot be redone
with different parameter setting later. Hence, we recommend recording of sufficient
amount of sample data to at least trim the SED-parameters. In SonarX trimming can be
done during the conversion the recorded files. See section Improving SED by trimming the
criteria in Chapter 5-Converter. Sonar5 can redo single echo detection later as part of the
pre-analysis. See the Analysis = Pre-analysis=SED... menu.

Crossfilter detection
The Crossfilter detector (CFD) has been developed to improve the analysis of echosounder
data. The detector locates targets in the Amp echogram by the application of image
analysis. Detected targets from the CFD can be applied for improved single echo detection,
for tracking, for removing unwanted targets such as fish when plankton is the aim and for
improving max range detection. The CFD works on complete targets rather than on
individual pings, and utilizes both the signal from the targets as well as the surrounding
noise level in the detections. This makes the CFD to a powerful tool.
The detector can perform five different tasks.
a) Tracking (Analysis => Analysis => 1-setup => tracking => Crossfilter)
b) Single echo detection. (Analysis => Pre-analysis menu)

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c) Noise reduction (Analysis => Pre-analysis menu)

d) Max range detection. (Analysis => Pre-analysis menu)
e) Fish pen detection

The Crossfilter detector was initially designed to overcome the two main problems seen by
traditional single echo detectors based on echo length. The problems are missing echoes in
tracks and erroneous detections from fluctuations in the background reverberation. The
CFD will normally create tracks better suited for tracking with fewer ping gaps and less
erroneous detections surrounding the tracks. See chapter 19_Crossfilter detector for more
information.

Bottom detector and inspector

The bottom detector and inspector have a top control panel and two tabulated pages named
detector and inspector. The detector deals with bottom detector methods and parameters.
The inspector assists in inspection, editing and correction of a detected bottom. This
section describes first the top panel, then the detector page followed by a description of the
inspection page
Bottom detector and inspectors top control panel

Figure 21. The bottom detector dialog’s top control panel.

The top panel has three buttons and three check selectors. The buttons can start the auto
detection algorithm, open the popup menu and ask for this help text.

Auto detect button

Start detection of bottom. The method described at the Detector page will be applied.
Process all selected files checkbox
Turn this on to process all files selected in one of the file open menus. Turn off to process
only the visible file. When the parameters are trimmed and the bottom detector seems to
manage the detection well, the option let you run the detector on all file or a selected subset
set of files in the working folder.

Work on entire file or visible part

This selector determines if an operation such as detection, test or adding a margin shall be
applied to the entire echogram or to the visible part. The selector is not available when the
Process all selected files checkbox is checked on. Operations will then be applied to the
entire files.
Menu Button
The menu button opens the flowing menu

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Save and load

The bottom definition can be saved and loaded to alternative filenames in case one want to
play with the bottom detection, but want to be able to load back the original bottom.
Export and Import
The bottom detector parameters can be exported and imported. The file for this is a plain
text file which can be opened in any editors such as word or notepad.
Command editor (S5 only)
The bottom detector writes commands to the command editor, and executes them. As an
alternative the operator may write commands directly to design new detectors or apply
option not available in the default detector. The Command editor will open this editor.

Bottom detector
The bottom detector defines the bottom line described in chapter 2, section Bottom. Note
that the bottom line is not the same as the bottom profile seen in the position diagram's YZ-
exact display mode. Note also that the bottom line simply is a way to tell the system that
we do not want to include samples or echoes at ranges outside the line. Thus, the bottom
line can be applied as an outer noise level line in a horizontal river application as well.

Bottom detectors method composer page

This page let the operator compos the detection process. At most, four steps can be applied.
They are Pre-filter, detection method, post-filter, and target remover. The left column
contain these options read from top to bottom.

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Figure 22. The bottom detector dialogs detector page set up to show all available tools and
parameters.

Show process step by step.

If checked, the echogram will display the result after each step in the process. The original
echogram will not be altered.
Pre-filter
It may improve the bottom detection if noise is removed by a low pass filter. Checking the
pre-filter check box will enable setting of the two the pre-filter parameters. The filter is a
running mean filter. Filter height defines the number of samples to average and Filter
width the number of pings.

Method selector
The method selector is located between the pre and post filter and contains three options,
Best candidate, Image analysis and Bottom up => Seaweed detection.

1) Bottom candidate detector

When selected, both the parameters and the additional parameters panels will be visible
and should be set. The parameter panels are located on the left side of the method
composer page. The candidate detector consists of a candidate detector and a score
algorithm. The candidate detector obtains a set of possible bottom candidates based on the
threshold and the echo length criterion. Initial points are given to each detected candidate
based on the shape and strength of the candidate. A score upgrade function evaluates new
candidates by looking for candidates in the previous ping. If fore example, a new candidate
is located at 30 m and the gate parameter is set 0.3 meter, then a candidate in the previous
ping will be inside the gate if it is located somewhere between 29.85 and 30.15 meter. The
system uses two gates, one small and one large. The score of new and existing candidates
are upgraded depending on the whether they are located outside or inside these gates. In
the end, the candidates with the highest score are selected.

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Problems with the best candidate detector

The detector may be fooled by fish, fish schools and noise spikes. If this is the case, the
filters and the target removal may help. Another common problem is that the detector tends
to find the solid rock bottom below e.g. a layer of mud or below a layer of stronger echoes
looking like the bottom, but caused by the side of the beam hitting part of steep hills. In
such cases we recommend to select the Image analysis method rather than the bottom
candidate method. Another possibility is to apply the post-filter. Applying the post filter
will most probably result in detection of the first occurrence of the soft bottom rather than
the hard and stronger signal from the rock below.

2) Image analysis detector

When Image analysis is selected, the bottom detector will tempt to remove all targets
except the bottom echo. In the end of the process the method will search from the start
depth defined in the min range parameter and down to the depth defined by the max range
parameter. The first echo found on the way from min to max range will define the bottom
in that ping.

The Image analysis detector works very well in most situations because bottom is a strong
and long target. It is strong in the sense that it is stronger than the noise level, and it is long
in the sense that it or part of it is seen in more pings than any fish and fish schools. The
threshold parameter should be set so that all targets including bigger fish and bottom
should be well seen but so that background noise is suppressed. The remove small targets
should be set to a value larger than the max number of ping or track length of each non
bottom targets.

3) Bottom up
Same as above, but the detector starts searching from the fare end of the echogram and up
towards the transducer. This can be useful if the detector tend to detect fish schools and
thermo-clines as bottom.

Post-filter
This filter will smooth the detected bottom. This may improve the detection. Checking the
post-filter check box will enable setting of the two the pos-filter parameters. The filter is a
running mean filter. Filter height defines the number of samples to average and Filter
width the number of pings.

Remove small targets checkbox

Fish and fish schools can fool a bottom detector. Since these objects normally are shorter
than the bottom measured in number of pings, we can remove these targets before we
apply the bottom detector algorithm.

Bottom detector parameter panel

Threshold parameter
Only echoes stronger than the threshold will be regarded as bottom candidates.

Margin

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The margin has nothing to do with the detection. It is simply a value that will be added to
each detected depth. Use this to adjust static trends in the detections. As an example, if the
margin is set to 0.05, this value will be added to each of the depth detections before they
are stored on disk.

A constant value can also be added to correct for static trends after the bottom have been
detected. See the description of the Margin button later in this section.

The bottom line can also be lifted or lowered with the temporary margin function located
in the echogram control dialogs Layer, Bottom page.

Note that SonarX has three items named margin. The margin edit box described her, and
the margin button at the bottom detectors inspector page, add a constant value to the
bottom detections in a file. The margin found in the echogram control dialogs Layer,
bottom page is a temporary margin witch enable quick lifting or lowering of all bottom
lines for all echograms that are opened. This margin is stored globally in the systems
configuration file and not in each individual echogram bottom file. See Margin in chapter 7
in the Layer and Bottom section.

Min range, Max range parameter

Multiple echoes are located within the range indicated by the min and max range
parameter.

Bottom detector additional parameter panel

This panel contains additional parameters used only by the best candidate detector. The
panel is visible only when the best candidate method has been selected in the method
composer.
Min. Echo length parameter
Only echoes longer than this criterion are regarded. Echo length is measure from the start
level to the stop level relative to the transmitted pulse length.

Start level
The level, relative to the peak, where the echo length is measured from.

Stop level
The level relative to the peak, where the echo length is measured to.

Min gate parameter

Gates are applied when the main bottom detection algorithm compare a bottom detection
with detections in surrounding pings. Gates are estimated automatically by the system. At
short range this estimate may be too small. If the estimate is smaller than the min gate
parameter, the gate estimate is overruled by the min gate parameter value. When set to e.g.
0.2 m, the gate can be larger but never smaller than 0.2 meters. The system applies two
gates defined by the range and the Min. gate parameter.

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gate s  0.01  Range

if gate s  min . gate then gate s  min gate
gatel  3  gate s

Subscript letter s and l indicates small and large gates respectively.

Bottom inspector
The bottom detectors Inspector page enables manual editing or automatic fixing of the
detected bottom line. An automatic detector may not always produce exactly the result one
wants at all places. High intensity just above the bottom line or large steps or jumps in the
bottom line may indicate errors such as missing bottom or that the line is set below the
actual start of the bottom echo.

Figure 23. The bottom detector dialogs Inspector page. The dialog can be accessed from
the Analysis =Pre-analysis menu or from the echogram’s bottom menu.

List box report

The lower left list box reports the result of test. Clicking a line here will bring the
echogram to that place for inspection. Only the first occurrence of a problem is reported.

Chart report
The Lower right chart plots the tested problems as a function of ping. Here all problems
are plotted and not only the first occurrence as reported by the list box
Test button
The test button starts the testing according to the selected test page to the left for the
button. If the step page is selected step test will be carried out. If the intensity page is
selected, intensity test will be carried out.

The All pings or Visible in echogram selectors at the top of the dialog selects whether the
test shall be carried out on the visual part or the entire part of the echogram.
Fix button
The Fix button starts the testing according to the selected test page to the left for the
button. If the step page is selected step test will be carried out. If the intensity page is
selected, intensity test will be carried out.

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The All pings or Visible in echogram selectors at the top of the dialog selects whether the
test shall be carried out on the visual part or the entire part of the echogram.

Memorize button
This provides a short time memorizing of current bottom. Press the button to store the
current bottom line in memory if you suspect that you may like to go back to the current
bottom after playing with the edit or fix. The memory will be erased if the file is closed.
For long term storing, save the bottom to a separate file with the save menu accessed from
the top menu button.
Recall button
Press this button if you want back an earlier memorized bottom.
Margin button
Margin button will open a dialog that will ask for a constant value to add to the bottom
detections. It will depend on the selectors in the bottom detectors top control panel whether
the value will be added to a multiple set of echogram files, to the echogram file currently
seen in the echogram window or to a selected part of that echogram. Read also about the
temporary Margin in chapter 7 section Layer and Bottom
Edit button
The bottom editor can be used either to fix an error in the result from the auto detected
bottom or to draw the entire bottom. Press the edit button, move the mouse into the
echogram, press left mouse down, and move the mouse with the left mouse button pressed
will do. To end the edit operation, it is important to re-click the edit button. Re-click will
turn the cursor back to default and save the edited bottom line.

To draw the entire bottom, it may be an idea to first compress the entire echogram into one
visible page, and then afterwards inspect and correct the result by moving through the
echogram in normal or zoomed mode.
To use the manual editor to fix errors in the detection, it may be a help to click on one and
one step registered in the list box, fixing each step manually with the bottom editor.

Step test page

When the Step page is selected, the Test and Fix buttons works on steps. The “All pings”
or “Visible in echogram” selectors at the top of the dialog selects whether the “Test” or
“Fix” shall work on all pings or only on the visible part of the echogram. The Step panel
holds two controls.
 “Report steps greater than [ 200 ] cm” This is the step threshold. Only steps greater
than 200 cm will be reported. 200 cm is the default, but user can change this.
 “Fix step by copying [ 5 ] successive detections” This statement will cause the last
bottom detection before a reported step to be copied into the next five pings. 5 is
default but can be changed by the operator.

Intensity test page

When the Intensity page is selected, the Test and Fix buttons works on intensity. The “All
pings” or “Visible in echogram” selectors at the top of the dialog selects whether the
“Test” or “Fix” shall work on all pings or only on the visible part of the echogram. The

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Intensity panel holds two controls.

 “Report if intensity > threshold in range bin [ 1 ] above the bottom line” Threshold
is the threshold seen in the Amp-echogram. Range bin refer to the range covered by
one sample. Range bin 1 is the first bin or sample above bottom. 1 is default, but
the user can change this.
 Set threshold button. This button opens the TS distribution dialog. Here, set the
“Start from” to the threshold you want to work with, and press the Apply to update
all thresholds in the system.

Dead zone page

This page let you apply or remove the dead zone. See also description in the section
Error! Reference source not found..

Heave correction

Figure 24. Heave correction dialog.

If the Apply heave sensor is checked, the input from a heave sensor will be applied for the
correction. Otherwise the heave correction method will use the detected bottom line. The
line is smoothed and the difference between the smoothed and the non smoothed bottom
line is applied to correct the echogram and tracked fish. Factor is multiplied to the
difference and should normally be set to 1.

The run button will process generate a new, corrected echogram file according to the
selected run option. The new file will have an additional Q in the extension to avoid
overwriting the original file. The Test button will carry out the test selected in the test
option panel. Only the visible part of the echogram will be processed and zooming is
allowed.

See the HeaveCorrection command in chapter 15 for more information.

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Flat bottom echogram

Figure 25. The flat bottom dialog is opened from the main menu Analysis=>Pre-analysis
This menu opens a dialog similar to the heave correction dialog. The method uses the
defined bottom line to produce a flat bottom echogram. Thus, a bottom line must be
available. The test button will generate a preview of the result without actually creating a
new echogram. The Run button will generate a new echogram with the same filename as
the original echogram file but with an additional letter Q added to the extension. The new
file will not be opened unless the Open result checkbox is checked. If the Generate
commands only checkbox is checked, a set of commands is written to the tracker windows
image analysis command editor. The generated commands are described in chapter 15.
Depth offset edit box
The depth of the new bottom will be set to the average of the bottom line plus the value
applied in the depth offset edit box.
Options selector panel
Save corrected echogram
Correct range for tracks in fish baskets
Both tasks above.

ES60 correction implemented

ES60 has a systematic error. The error consists of an overlaid triangle pulse causing the
received power to increase and decrease relative to the actual echo returned from the water.
(Ryan T., Kloser R., 2004) describes this error and proposes that it can be identified from
the ringing pulse seen in the beginning of each ping. The period of the error signal is 2721
pings and the amplitude of the pulse is also fixed. What is not known is the start of the
error signal. We have implemented an auto-correlation algorithm to find the most probable
start of the triangle error signal and correct the file according to this.
Where to find the correction method
The ES60 error correction dialog is opened from the main menu Analysis => Pre-analysis
=> ES60 error correction

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Figure 26. The ES60 error correction dialog is opened with the main Analysis/Pre-
analysis/ ES60 error correction menu.

Items on the main correction dialog

From (m)
This edit box defines the start range for the integration.
To (m)
This edit box defines the end range for the integration.
Chart
The chart in the bottom of the dialog can present the correction function and the integral
from the file. It can also present the integral pulse from all teh file or from a selected
number of pings. What to see in the chart is controlled from the tabulated manual and the
tabulated tools page.

Automatic correction

Figure 27. Items on the automatic correction page.

Select files button
This button enables selection of a set of files to be corrected.
Do not correct if error > 5.23
The number is user defined, and prevents automatic correction of badly auto correlated
files.
Start correcting button
This button will start the correction process. The algorithm will integrate the echo intensity

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from ping 1 to ping 2722 ping by ping and then remove the DC level. This revel the files
triangle error without any offset intensity. An artificial triangle pulse is auto correlated
against the measured error signal to find the best fist. The square root of the sum squared
error is stored. Then the algorithm moves “Auto correlation step” further and repeats the
process. When the total file has been processed, the start of the triangle pulse is obtained
from the sequence that gave the lowest auto correlation error. The total file is then
corrected before the process goes on to the next file. A result table is presented when the
process has finished treating all selected files.

The operator can define an error threshold. If the error is higher than the user defined error
threshold, the file will not be corrected. The operator can then open the manual correction
methods and study the signal end the optimal / most noiseless part of the ringing pulse
before performing the correction.
The operator can also define how many pings the system should jump between each
probing for optimal auto correlation. A small number increases the chance for good results,
but results in a slow process when files are large.

When the correction algorithm is finished a correction report will be presented.

Example of ES60 correction report:

Status Error Filename

---------------------------------------------------
Corrected 1.32 L0007-D20040619-T062629-ES60_R_0-30.uuu
Corrected 1.36 L0008-D20040619-T080014-ES60_R_0-30.uuu
Not corrected 7.00 L0008-D20040619-T090015-ES60_R_0-30.uuu
Corrected earlier -1.00 L0008-D20040619-T10001-ES60_R_0-30.uuu
Corrected 2.30 L0008-D20040619-T11000-ES60_R_0-30.uuu

Status “Not corrected” is given because the file had a higher error than the error threshold
set by the operator.
Status “Corrected earlier” means that this file has been corrected before. Individual files
will remember that they have been corrected.
Manual correction page
The methods here are designed to help the operator if it proves difficult to obtain good
results with the automatic method. Note that the automatic method simply starts a batch
job pressing the buttons in the following sequence:

1. Search button,
2. Correlate button,
3. Correct file button
4. Next file button

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Figure 28. Items on the manual correction page.

Correlate button
Pressing this button will correlate the integral starting from the ping number seen in the
From ping edit box and 2721 pings ahead. Correlation error will be estimated and the fitted
pulse will be presented together with the integral pulse in the main chart.
Correct file button
will use the displayed correlation to correct the file. One should not press this button if the
correlation is low or before the correlation button has been pressed.
Next Prev file buttons.
After having corrected the a file it is natural to open the next file. Sonarx has keeps a list of
file one want to work with. If only one file have been selected, pressing the buttons will
ask for more files. As an alternative to using the buttons, Alt+F, Alt+N, Alt+P or Alt+L
keyes can be used to jump to the first, next, previous or last file. See also the main File
/quick file open menu.
Find the best ping start panel
It may be that there is noise in the first part of the file. The scrollbar and the edit box in this
panel let the operator check other parts of the file. Scrolling the scrollbar or typing a ping
number will present the integral of the triangle pulse from that ping in the dialogs bottom
chart.
The search button will automatically search for the best or most noiseless part of the file.
This will be done by performing the autocorrelation on sequences starting with increasing
ping numbers. The step edit box indicates the number of pings to jump between each
probing.
Correlation error gauge and label
shows the resulting auto correlation error
Manual correlation scroll bar.
Moving this scrollbar moves the artificial triangle error pulse relative to the integral pulse
from the file. Hence the operator can move the pulse until best fit is seen in the bottom
chart or on the gauge and error label.
Oscilloscope button
This button opens the oscilloscope in time mode. The operator can click at a range in the
echogram window and will then see the intensity at that range for the pings presented in
the echogram. If the echogram is compressed (Alt+z key when the echogram is active), to
show all pings, the total triangle signal can be presented. Changing the oscilloscope
windows display mode enables studying the ringing pulse in range mode to find the best

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part to integrate.

Tools page

Figure 29. Items on the tools correction page

Pressing the Plot button will plot the integral from the pings noted in the From and To ping
edit boxes. The range to be integrated is defined on the left side of the dialog.

Analysis
Different analysis methods are implemented in different windows. Selecting an analysis
method is a question of selecting the correct set of windows. One can either use predefined
templates that set up a selection of windows for each kind of analysis or one can modify an
existing setup by adding tuning or removing windows. Both the analysis =>Setup menu
and the Analysis Analysis=>Analysis=> Setup menu can be used to setup and modify
analysis.

Figure 30. Analysis => Analysis menu

Setup, adding and removing analysis

Adding analysis
The Add menu provides items for adding tracking, biomass or macrophyte analysis to an
existing setup without rearranging or removing the existing setup. This enables the
operator to mix different analysis windows such as biomass and tracking or different
biomass estimation methods.

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Removing an analysis
The remove menu has options for removing individual analysis without changing other
methods. Removing tracking analysis will take away the tracker window, classification
window and position diagram windows without removing biomass macrophyte windows.
Setup
Selections in the Set-up menu will close all previous defined windows and set up the
system according to predefined templates. The computer measures the screen and sizes the
windows to fit the screen in an optimal but predefined way. Variables such as threshold
may be set as well.
Making your own setups
Whenever a desired setup has been obtained, this setup can be saved to file with the
File=>Setup menu. The echogram control dialogs Save button can save the setting for a
special echogram adjustment without influencing on the rest of the system. .
1-Setup dialog
Clicking this menu will open a dialog from where the various methods can be set up,
added, or removed. Select a method and click the ok button will apply and close, while the
apply button will set up the system and leave the setup dialog on the screen for later use.
1-Setup => Biomass
This menu sets up the system for biomass estimation. Sonar4 can select biomass based on
single echo detections, which will set up the screen with one echogram window and one
biomass window. For Sonar5, a second option;- biomass based on tracked fish, are
available. This will set up windows both for tracking and biomass estimation. It is possible
to track fish and do the biomass estimation at the same time, but we recommend that one
first do the tracking and then focus on the biomass estimation. See chapter
08_Biomass.doc for more information.

1-Set up => Tracking

The Analysis = 1-Set up= Tracking menu contains four different tracking set-ups, from
simple tracking to image analysis-based tracking. Simple tracking is available in Sonar4
while all methods are available in Sonar5.
Simple tracking
Selecting simple tracking will close all opened windows and adjust the system for simple
tracking. An echogram window and a position diagram window will be opened. Additional
position diagram windows can be selected in the Analysis =Data insight menu.
With this method, echoes are combined into a track manually with the mouse in the
echogram. The combined echoes form a track. The individual echo positions and track
features can be studied numerically and graphically from all aspects in the position
diagram window. Tracks can not be stored, but a note can be generated in the advanced
sonar parameter dialog's description page.
To generate a note, open the dialog from the main menu: Utility => Description of the
sonar file and double click in the echogram at the position of the fish. This will write a note
about the position of the fish in the dialog's memo.

How to do simple tracking:

a) Select "Analysis => 1-Set up => Tracking => Simple" from the Analysis menu.
b) Draw rectangles around the echoes to be combined in the echogram.

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c) Draw a freehand line around a region in the echogram. (Press the F-key when the
echogram is active to enter and leave the free hand selection mode).

See the section Tracking_Control_Menu and the section Analysis_started_with_mouse in

chapter 6 Echogram window for more information about combining echoes into a track.

Standard tracking
Standard tracking set up the system for manual or automatic tracking, but in a very
simplified way. There will be no classification window, only one possible fish basket for
track storing and only simple auto tracking parameters. Track features are restricted to a
small predefined set.

Manual tracking
Manual_tracking is described in chapter 12. Selecting the menu closes all opened windows
and adjusts the system for manual tracking. This involves an echogram window, a position
diagram window, the tracker window and the classification window. Tracks can be
combined and studied in the same way as with simple tracking but they can also be
classified and stored. From stored tracks, track statistics can be generated.
Automatic tracking
Automatic_tracking is described in chapter 12. Selecting the menu closes all opened
windows and adjusts the system for automatic tracking. This involves an echogram
window, a position diagram window, the tracker window and the classification window.
Tracks can be combined and studied in the same way as with simple tracking but they can
also be classified and stored. From stored tracks, track statistics can be generated. The
auto-tracker can be set up in various ways from simple auto tracking to advanced tracking
including four different methods for track support, prediction, gating and association.
Crossfilter tracking(CFT)
Tracking_Crossfilter is described in chapter 12. Selecting the menu closes all opened
windows and adjusts the system for Crossfilter tracking. Tracks are located in the
amplitude echogram and single echoes within detected regions are combined into tracks.
Tracking performance
Tracking_Performance opens a window where one can study the effect of the different
tracking parameters and graphically. Here one can see how a specific tuning of the auto
tracker will treat the different tracks in the file. Note that the tracker has a separate button
for automatically detecting the best tuning of the tracker in the advanced mode. This works
by first tracking a few tracks manually, and then pressing the auto parameter button. The
tracks will be analyzed to find the optimal tracking method and its parameter setting.

Result control
This selection re-arranges the windows on the screen to ease traversing and studying of
stored tracks.

1-Set up =>Macrophyte
This menu item will set up the system with one echogram and one Macrophyte window.
The macrophyte analysis has tools for detection and editing of macrophyte roots and tops.

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When roots and tops have been detected, the window will estimate parameters such as
Biovolume, Bioarea, and macrophyte heights each time a region is selected on the
echogram or by the echogram control dialogs analysis page. Macrophyte analysis is
described in the section Macrophyte analysis later in this chapter
1-Set up Multi frequency analysis
This menu item opens the multi frequency setup dialog. The dialog enables composing
various setups and do also contain some of the analysis tools. See chapter 23 Multi
frequency analysis.

Select region to be analyzed

Layer control dialog
opens the echogram control dialog at its layer, bottom and noise page.
Single file analyze control dialog
opens the echogram control-dialog at the Analyse page. See chapter 7.
Multi file analyze control dialog
This opens an analysis control dialog that can apply constant ESUs or segment in various
ways, and with Ping, time distance and file as unit. This control dialog enables variable
layer thickness and individual layer placement. Layer can be both bottom and surface
related. Multiple files can be selected and analyzed in one go when the analyze button is
pressed.

(Hint: A region....
This menu item is simply a text message placed here as a reminder.
It is important to tell the system what it should analyze. What to analyze is described as a
region consisting of from and to ping and from and to range values.
Regions can be defined or selected in the following ways

1) Drawing a rectangle directly in the echogram. To cover more than displayed by the
echogram, increase the echogram compression as described in the section Zoom and
compress in chapter 6-Echogram. See also the section Analysis started with the mouse
in the echogram in chapter 6-echogram menu.
2) Defining a rectangle in the Analyze control dialog. See the Analyse_control page in
chapter 7.
3) Defining a subset of rectangles within the selected rectangle in the Analyze control
page. This applies only to biomass estimation.
4) Free hand drawing. The region to be analyzed can be selected by drawing a free form
line around the region to be analyzed. Selecting “Free hand selection” in the echogram
menu switches between free hand and rectangle selection..
Modifying and restricting the selected region
 Pelagic layer: Restricting the analysis to a pelagic layer will overrule the range defined
above. The analysis will be carried out between the selected pings within the defined
layer lines and not between the originally selected ranges.
 Bottom line: When the bottom line is visible, the part of a region defined below the
bottom will be restricted by the bottom line.
 Bottom layer: Restricting the analysis to a bottom layer will overrule the range in the

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defined region so that only the region in the bottom layer is displayed.
 Erasing echoes can be applied to avoid analysis of certain parts of the echogram.
Layers
Layers are applied to restrict analysis to specific ranges. As soon as a layer is turned on, all
analysis will be restricted to that layer. If the layer is defined at a range not currently
displayed by the echogram window, starting an analysis will bring the layer into sight.
Parameters and checkboxes controlling the layers are located in the echogram control
dialog's layer bottom and noise page. See the section Layer and bottom control page in
chapter 7. Parameters controlling sub segments and sub layers for the Biomass analysis is
located in the echogram control dialogs analyze control dialog. See the section Analyse
control page in chapter 7. Layers can also be controlled from the echogram windows Layer
menu in chapter 6.
The system defines the following layers
a) Constant pelagic layer
A constant pelagic layer consists of two horizontal lines seen in the echogram window. If
the pelagic layer is on, analysis will be restricted to this layer. Biomass analysis can divide
a pelagic layer into any number of sub segments and sub layers. The layers and segments
will be of equal thickness.

b) Variable pelagic layer

Pelagic layers are constant in range. If one wants to define a pelagic layer with variable
range one can use the bottom line. Draw the bottom manually with the mouse wherever
you want to define the lower part of the pelagic layer. Then turn on the bottom layer and
adjust the thickness of the layer. As an alternative, lift the auto detected bottom line up into
the water with the margin parameter and eventually modify parts of the line with the
mouse. See bottom and bottom layer for more information. A variable pelagic layer can be
divided into sub segments, but not into sub layers. Reduce the layer thickness and redo the
analysis at different ranges to analyze multiple layers.

c) Bottom layer
A bottom layer consists of a line following parallel to the bottom line. To see the bottom
layer the show bottom checkbox must be checked. The distance between the bottom line
and the bottom layer line is controlled by the layer parameter. In addition, the bottom-line
and thereby the bottom layer can be lifted up and down by the margin parameter. When the
Biomass analysis is restricted to a bottom layer, the analysis will be divided into the
requested number of sub segments, but the number of requested sub layers will be
overruled and set to 1.

Variable layer thickness

A pelagic layer can be divided into a set of equally thick sub layers simply by setting the
number of sub layers in the echogram control dialogs analyze page. This enables fast
operation. To analyze a file with layers of variable size, define a layer at one depth with
one thickness and do the analysis. Then move the layer up or down and change the
thickness before starting the next analyze. Store the result in the biomass basket by
pressing the A-key in the biomass window or export the result to a spread sheet after each

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analysis.
Restricting the analysis to layers
If a pelagic or bottom layer has been defined, the selected region will be restricted to
analyze only the ranges defined by the layer. Selecting a region as described above will
then select the pings, while the layer will overrule selected range.

Why do I not see the layer lines?

 No layer has been selected in the show layer panel.
 Colors or thickness of the layer line are set so that the layer lines are difficult to see.
 The echogram window is zoomed to a range where no layers are defined.

All mentioned components are located in the echogram control dialogs layer bottom and
noise page. See section: Layer_and bottom and the Analyse control page in chapter 7, and
the Layer_menu section in chapter 6.

Start analysis
Starting an analysis is a question of informing the enabled analysis windows about the
selected region to be analyzed. When the region is selected with the mouse directly in the
echogram, the message about the selected region will be broadcast as soon as th left mouse
button is dropped. If a region is selected in the echogram control dialog's analyze page, the
defined region is broadcast when the analyze-button is pressed. If a Biomass window has
been opened the Biomass window will receive the message and analyze the selected
region. If a position diagram window is available, tracking will be performed and the
position of the tracked single echo detections will be displayed.
See also the section Analysis started with the mouse in the echogram in chapter 6-
echogram menu.
Single file analyze control dialog
open the echogram control dialog at the analysis page where the one can use the Analyze
button to start an analysis.
Multi file analysis dialog
open the multi file analyze control dialog. Pressing the analyze button will analyze all
selected files.

Analysis methods
Tracking
Tracking is described separately in chapter 12_Tracking

Biomass estimation
Biomass estimation is described separately in chapter 8_Biomass

Macrophyte analysis
The Macrophyte analysis window can perform ESU based, and depth based analysis.

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The number of ESU’s or depth layers to be presented is selected in one of the two analysis
controller dialogs.

ESU analysis output macrophyte features versus position, ping or time. Depth analysis
output the macrophyte features versus depth. Macrophyte analysis is located in the
Analysis menu. The analysis applies to vertical mobile surveys on relatively flat water with
fairly vertical transducer mounting. Transducer and base platform motion
(Utilities=>Parameters =>Application) are not included in the calculations of the
macrophyte estimates, but warnings are given if pitch and roll are applied in the Utilities
=> parameters=> application menu and exceeds +/- 5 deg during an analyzed segment.

Figure 31. Macrophyte analyse window

Figure 32. Zoomed flattened echogramshowing macrophyte echoes framed by the

macrophyte top line and the macrophyte roots line. The analysis uses the lines to find
biovolume, area, sv etc.

Three steps
Macrophyte forms a layer with variable thickness above the bottom. Analyzing this layer is
divided in three operations.

1. Detecting, editing and accepting a line defining the roots of the macrophyte.
2. Detecting and accepting a line defining the tops of the macrophyte.
3. Estimating the amount of macrophyte between the detected tops and roots for a
number of pings or a sailed distance.

Detections of the roots and tops may be the most difficult part of the analysis. Automatic

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methods may or may not work well. This depends on the nature of the data influenced by
the macrophyte itself, the consistence and depth of the bottom and the echosounder
properties. It may be necessary to correct the results from the automatic detection
algorithms with manual editing.

Detection of the roots and tops may be improved by flattening the echogram. See the
section Flat roots echogram
GPS data is needed
Note that navigation data must be available for this method to work correct. Navigation
data are stored during the survey. If navigation data was not stored, for example due to a
defect GPS, Artificial GPS data can be feed into SonarX in the advanced file open dialog.
Detecting macrophyte

Figure 33. Tools for detecting and presenting macrophyte tops and base (roots). Roots are
the same as base indicating the point where the plant meat the bottom.

The tools for these operations are seen in the upper left side of the Macrophyte window.
There are two sets of detection tools, one for detecting the roots and one for detecting the
tops.

The detect / edit buttons will prepare the system for detections and open the bottom
detector. See section “Bottom detector” in the manual’s chapter 4 for a description of this
detector. The bottom detector enables manual editing and automatic detection of the
macrophyte roots and tops.

Use the bottom detectors method composer to set up the detector and press its Auto detect
button. Study the resulting bottom line in the echogram and trim the method until the
bottom line defines the roots of the macrophyte as well as possible. Zoom the echogram in
on difficult regions to verify that the quality of the detection. It may be necessary to edit
parts of the line manually. To do so press the edit button on the bottom detectors first page.
To locate insufficient detections, the step function and the step list on the detectors first
page may be a help. Clicking on a reported step in the step list will bring the echogram to
that position.

The accept buttons will accept the detected lines and the applied detection parameters.
Hence, next time one press the Detect roots button the detector will be set up with the
detection parameters for the roots.

The color panels and the number editors define the color and thickness of the lines that will
indicate the macrophyte roots and tops. Click the panels to change the colors, and edit the
thickness to define the thickness of the lines. This can be done both before and after the
lines are detected type the thickness to def defines the color of the in Figure 31.

The visible checkboxes controls whether the macrophyte tops and roots lines are visible.

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During detection / editing of one line, the other is invisible by default. Check the visible
checkbox to see the line also during editing.

Hint on detection
The bottom detector has three main methods located in the bottom detectors method
composer page. They are 1) Best candidate, 2) Image analysis and 3) Bottom up. In many
cases, method 2 and 3 works better than the best candidate method. When using 2 and 3,
the threshold becomes important. In cases where the roots have a higher intensity than the
bottom under, applying the bottom up detector with a threshold that separates the roots
from the bottom may work well. If the bottom under the roots reflect more that the roots,
method 2 may be the best. Set for example the threshold to -40 for root detection and to -
70 to detect the macrophyte tops. Click on the echograms color bar and set the threshold to
find what threshold to apply.
Echoes from fish
Strong echoes from fish may be detected as well, making the root detection to jump up and
include fish. This can be avoided by removing the fish. Fish can be removed with the tools
located in the bottom detectors remove small targets panel.
More fish removing tool
If unwanted targets are a main problem for the detection, they can be erased with the noise
reduction system located in the Analysis=>Pre-analysis menu. They can also be erased by
the manual eraser tools located in the echogram menu and the echogram control dialogs
noise page.

Height threshold
A threshold can be set on the macrophyte height. Only pings where the macrophyte is
higher than the applied height threshold (h > thr) is applied in the analysis.
A threshold introduces a question about numbers of pings involved in the calculation of the
mean values. Total number of involved pings (N1), and number of pings where the height
is above the threshold (N2).

Setting up and starting the analysis

Data can be analyzed in units of pings or in units of sailed distance. The selected pings or
sailed distance can be divided into a number of sub segments.
There are two ways to select and start the analysis.
a) Select the pings to analyze directly in the echogram with the mouse.
b) Press the analyze button in the top panel to open the echogram control dialogs
analyze page. Here set up the analysis and press the echogram control dialogs
analyze button. See section Analyze control page in Chapter 7 for more information
about this.

ESU analysis
ESU analysis is selected with the ESU radio selector in the top of the Macropyte window.
ESU is short for Elementary Sampling Unit. An ESU is the same as a segment. ESU can be
measured in pings, sailed distance or time. When selected, the chart will plot ESU versus
the selected macrophyte feature. The export menu found in the macrophyte windows
popup menu (right click with the mouse or press the menu button) will export plant

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features versus ESU.

Depth analysis
Depth analysis is selected with the Depth selector in the top of the Macrophyte window.
The depth analysis sorts the analyzed ESU’s according to average plant depth in each ESU.
The results are then binned according to the layers set up in one of the two analysis
controllers. If the first layer has been set up to start from 4 meters and the layer thickness is
set to 1 meters, then results shallower than 4 meters will be discarded. The layer between 4
and 5 meter will show the average and max results from all ESU’s mapping to this depth
and so on. If the ESU’s have been is set up to cover 10 ping each then all estimates in the
depth analysis will be based on 10 pings. Depth will be the average depth for the 10 pings.
Plant height will be the average of the plant heights found from the same 10 pings. To
obtain depth results from individual pings, the analysis controllers have to be set up to
analyse ESU’s or segments of 1 ping each. For analysis controller I one must set up nr of
sub segments to equal the number of pings to achieve this. For the Analysis controller II
one can select ping based analysis and set each ESU to cover 1 ping.

Max plant depth

The Macrophyte window will always report the max plant depth in the window caption
independent of what kind of analysis one have selected. The dept is the base of the plant.

Elliptical transducers
Volume and area estimations are calculated from the wedge formed by the athwart ship
opening angle. Thus, for elliptical transducers, it is important to tell SonarX about the
transducers rotation. This is done in the parameter dialogs, application page. Check that the
application is vertical mobile and that the transducer rotation is set correct according to
how it was mounted on the boat. The parameters are found in the
Utility=>Parameters=>Application menu.
Flat roots echogram

It may be easier to define the macrophyte roots and tops if the depths of the roots are laid
out in a straight line. To do so, carry out the following steps.

1. In the panel named Roots, press the Detect / Edit button and detect the roots in the
original echogram
2. In the panel named Roots, press the Accept button

3. In the panel named Tools, press the Flat roots button

4. Repeat 1 and 2 if fine tuning of the roots in the new flattened echogram is needed

5. In the panel named Tops, press the Detect / Edit button and detect the tops in the
new flattened echogram
6. In the panel named Tops, press the Accept button

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7. Analyze data

Pressing the Flat roots button located in the Macrophyte windows left panel after the roots
have been detected and accepted, will estimate the average root depth and reorganize the
echogram to present the roots on a straight line at the average root depth. The number edit
box on the side of the Flat root button will add an offset to the average depth. This can be
necessary if the average depth is too shallow for some high macrophyte at deeper water.

Figure 34 Echograms before and after flattening.

Note 1. What about range when the echogram has been flattened?
The depth presented in the echograms caption, the estimated depth, bioarea and biovolume
for the macrophyte will be correct. The range bar on the side of the echogram will continue
to show the depth as it was for the original echogram. The range parameter set in the
bottom detector and the range seen in the echogram control dialog will relate to the depth
seen in the range bar and not to the actual range changing from ping to ping.
Note 2. Flat bottom makes a new echogram
When the Flat root button is pressed, a new echogram will be generated and opened. The
new echogram will have the same name as the original, but a Q will be added to its
extension to indicate the echograms processing level. The original echogram is still
available. Pressing the Alt+0 key will open the unprocessed echogram. Pressing Alt+1 will
open the echogram with one Q in the extension and so on. See the top file menu’s Quick
file change menu item for these short keys.
Preserving the old bottom definition
An eventually existing bottom line will be reorganized both by the detect roots and the
detect tops buttons. To preserve the bottom line, use the “Echogram=> Bottom=> Save
bottom as” menu before pressing the Detect roots, Detect tops or Flat root buttons. Use the
“Echogram=> Bottom=> Load” menu if you want the old bottom definition back.
Popup menu

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Figure 35 Popup menu accessed by the right mouse button or the menu button
Help
The help menu opens this file
Export
The export menu has a submenu that can export analysis results and dump all macrophyte
roots and tops. See the Exporting data section in this help file .
Delete results
This menu item deletes all results obtained since the macrophyte analysis window was
opened or since it was used last time.
Event editor
This menu item opens the event editor. The macrophyte roots and tops lines definitions are
defined and stored as events. In the event editor they can be deleted or edited.
Set transducer depth
This menu item is a shortcut to the Application dialog handling the applications and
transducer placement.
Exporting data

Right click with the mouse button or click the menu button to open the popup menu. This
menu has an export menu for exporting data to clip board or to file.
Both the analysis results and a table with pin, tops, roots and geographical positions can be
exported.
Reported macrophyte features and estimates

The following estimated features rely on the mean sailed distance between pings,
transducer depth, transducer opening angle in the athwart-ship direction, and the
macrophyte root and top detections. The mean sailed distance between pings is found from
the GPS positions of the first and last ping in a segment divided by the number of involved
pings minus one.
Transducer depth
Transducer depth is set in the Application page opened by the “Set transducer depth”
option found by pressing the menu button. Alternatively, use the main menu:
Utilities=>Parameters=>Application. Transducer depth is added to the transducer relative
depths independent of whether the echogram is set up to present depths relative to the
transducer or to the surface.
Ping
Start and end ping for each analyzed segment

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# Pings
Number of pings involved. End ping – start ping
Accepted heights
This is the number of analyzed pings in a segment where the macrophyte height exceeds
the height threshold.
From position
GPS position of the first analyzed ping in the segment
To position
GPS position of the last analyzed ping in the segment
Sailed dist
Distance in meter between the first and last ping. Distance is found from the GPS
positions.
Boat speed
Average speed of the boat for an analyzed segment.
Mean root depth (MRD in meters)
The mean root depth is the mean depth of the roots measured from the surface for
macrophyte higher than the threshold.

1 b1
MRD   depth i | hi  Threshold
N i a
Where a and b are start and end ping in the involved segment and N is the number of pings
where the macrophyte height exceeded the threshold.
Mean bottom depth (MBD in m)
Mean bottom depth for the analyzed segment is independent of whether macrophyte has
been detected or not.

b 1 901
1 1
MBD   depthi
(b  a)  1 i a
e.g MBD   depti
(90  70)  1 70

Where a and b are start and end ping. In this case the operator has asked the system to
analyze from ping 70 to ping 90. The last ping is not included in the analysis. If the
analysis region is divided in two segments the first will include ping 70..79 and the second
will include ping 80 .. 89.
Mean Bioheight (MBH in m)
Mean Bioheight is the mean height found in the analyzed segment. The distance between
the macrophyte top and root line is summed for all involved pings in the segment where
the height is above the height threshold. The sum is then divided by the number of summed
heights.
1 b1
MBH   heighti | h i  threshold
N i a
Where a and b are start and end ping in the involved segment and N is the number of
summed heights and heights must be above the threshold to be summed.

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Max BioHeight (m)

Max BioHeight reports the largest distance obtained between the macrophyte top and root
line for all involved pings in a segment independent of the height threshold.
Area Investigated (AI in m2)
The investigated width for a ping is found from the triangle formed by the sound beams
half power opening angle (-3dB opening angle) and the root depth at that ping. This width
is multiplied with the average sailed distance between each ping in the segment. The
process is repeated for all involved pings except the last in the analyzed segment.

Ri  rootdepthi
b 1
AI   2 Ri tan( / 2)  DistPrPing
i a
Where θ is the athwart ship opening angle.
BioArea(m2)
This is the same as the investigated area, but calculated only for pings with accepted
macrophyte heights.

% Ar. Inh .(PAI)

Percent area inhabited (PAI) is found by dividing the BioArea with the Area investigated,
and multiplied by 100.

BA
PAI   100
AI

VolumeInvestigated (VI in m3)

The volume for each individual cube is found for each ping in the analyzed segment as the
product between the beam with, average sailed distance between a ping and the root depth
at the ping. All volumes are summed and reported as the Volume Invest.

Ri  rootdepthi
b 1
VI   AI i  Ri
i a

BioVolume (BV in m3)

BioVolume is found by summing up accepted BioAreas multiplied with the macrophyte
height at each ping.
b 1
BV   AIi  hi
i a
Where hi is macrophyte height above threshold for each individual pings

% Vol. Inh.(PVI)
Percent volume inhabited (PVI) is found by dividing the BioVolume with the Volume
Investigated multiplied by 100.

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BV
PVI   100
VI

Mean Sv dB
MeanSv dB is the Mean Volume Backscattering Strength (MVBS). Sv is found from the
samples located between the lines defining the macrophyte tops and roots. Each sample are
summed in the linear domain and divided by the number of located samples. Samples with
Sv below the echogram’s current threshold setting are counted, but do not contribute with
intensity. Erased samples and samples from pings with macrophyte height equal to or
below the height threshold are regarded as not existing. They do not contribute and they
are not counted.
 1 P2 1 b1 Sv / 10 
Mean SvdB  10log   10 i , j   
 N i  P1 j a 

Where P1 and P2 is the first and last ping in a segment. a is the echo sample related to the
macropyte top while b is the sample related to the macrophyte base or root in each
individual ping. N is the total number of samples involved.

Mean sa Area Scattering Coefficient

Mean sa is the Area Scattering Strength. Sa can have different units. The unit is selected in
the Sa unit selection menu accessed with the macrophyte windows menu button or with the
right mouse click popup menu. Depending on the unit the reported sa will be HASC
(Ha/m2), NASC (m2/nm2), or ASC m2/m2),

1 P2 1  b1 Svi , j / 10  
Mean sa  4   10   hi 

N i  P1  j a  

Where P1 and P2 is the first and last ping in a segment. a is the echo sample related to the
macropyte top, while b is the sample related to the macrophyte base or root in each
individual ping. N is the total number of samples involved. hi is the macrophyte height in
meter for each individual ping i.

Seabed classification
The seabed classification unit has been developed together with the Spanish group “Grupo
de Recursos Marinos y Pesquerías” led by
Juan Freire. Most of the features estimated by this module has been defined by the Spanish
group. Here the main work has been done by Noela Sánchez as part of her PhD at the
Universidad de A Coruña.

The Seabed Classification module calculates a set of features from the first, second, and
third bottom and exports these features together with position information. The exported

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data together with ground truth data can then be feed into a statistical package in order to
do the final classification.

Analysis preparation
1.
2.
3. Press the Bottom detector button in the Seabed classification window and use the
appearing bottom detector dialog to detect a bottom line. Ensure that the obtained
detected bottom line is deeper than the Bottom Foot 1 (BF1). If necessary, use the
bottom detectors margin parameter to lower the resulting line below the foot.
4. Press the Set layers button in the Seabed classification window and turn on the
surface layer and the bottom layer. The surface layer line is used to prevent the
feature detector from reacting on the transducer ringing signal, and the bottom layer
line is used by the feature detector to stop the search for the bottom foot 1 (BF1)
feature.

Feature definitions

τ 3τ
Attack & Release

BP Bottom Peak BP
Ringing
BD
A4/5, B4/5 points
Bottom
detection A2/3, B2/3 points

Surface layer B1/4 point

BL point points

BF
MW Bottom BF
MW
Min water Bottom Foot
Layer 1
meter
τ = Transmitted pulse length

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Seabed feature description

Start range (SR)
SR1 set equal to the user applied surface layer line.
SR2 set like BD1 + 4 Tau (pulse length)
SR3 set like BD2 + 4 Tau

Min Water (MW)

Data between surface layer line and bottom detection line is smoothed with a running mean
window ( user defined size). Then the MW point is located as the point where minimum
filtered Sv are obtained.
Range and original non filtered Sv value are reported.
MW.Range
MW.Sb

MW Integral (Mean Sv)

Integral of the water reflection intensity between MW and BD
 1 BD1 Svi /10 
MeanSv[MW..BD]_1  10 log 10  dB
 N i  MW 

StdSv[MW..BD]_1  10 log 
 1 BD 1 SvMean/ 10
 N  1 i 
10  10Svi / 10  
2

 MW 
The index _1 indicate the bottom number.

Bottom Layer One meter (BL0)

Bottom Layer One meter point. This point is always 1 meter above the range of BD
The system output the average energy in form of Sv from the rounded number of samples
between BD and BLO.
Sum can be found by multiplication with the number of involved samples. Involved
samples can be found from the exported range resolution with meter per sample as unit.
 1 BD 1 Svi / 10 
Sv  10 log
N
 10  

 i  BLO 

BD Bottom detection point

BD1 Bottom detection algorithm detect this point.
BD2.R = 2*BD1.R
BD3.R = 3*BD1.R

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BP Bottom Peak
The algorithm starts at the bottom line and search downwards. Max values are updated on
the way. If no max values has been found 3τ (τ = transmitted pulse length) after the last
obtained peak, the search finish. The max is taken as the bottom peak and the Range and
Peak are noted.

BF Bottom Foot
New 2010.01.19
BF is now the local min point found above the bottom detection (BD). It is found by
searching from the sample above BD and up towards the surface. No filtering is involved.
The algorithm runs toward surface as long as the next shallower sample has lower intensity
than the previous deeper one. If the intensity stops dropping and start to increase the
algorithm stops and report the last found minimum. If no local minimum is found in the BF
search window (BFSW), then BF= BD + (BD – BFSW div 2) . BFSV is set by the operator
in the seabed detector dialog Earlier it was named Margin.

A2/3, A4/5, B4/5, B2/3, B1/4

The algorithm search from the peak to each side of the bottom pulse until the stated ratio
between BF and BP.
NB! Linear interpolation is applied on the Sv values to find the exact range.

Example:
SbValue =BD.Sv + (BP.sv – BD.Sv ) * Ratio where ratio = 4/5 2/3 and 1/4

SbValue is the intensity value to search for.

Algorithm searches for the sample before and after this value and use linear interpolation
to find the exact range

Second Bottom
All features reported for the first bottom is repeated for the second bottom with an index 2.

BP2 is expected to be found at the double range of peak 1. The algorithm jump to the
double range and search for the peak one pulse length to each side to obtain the absolute
maximum.
BF2 Currently the same as BD2
The algorithm search for foot 2 between peak 2 and the double bottom line range.

Min Water 2 (MW2)

The algorithm search for the min water 2 value between the obtained peak 1 and the range
of the double bottom line.

and so on for the rest of the features….

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Attack and decay

AttackEnery -Hardness
Decay energy =Roughness
  c 
Attacksamples  round  
 Meter Pr Sample 
Decaysamples  3  Attacksamples

AI 1  BottomInde x
AI 2  BottomInde x  Attacksamples
DI1  BottomInde x  Attacksamples  1
DI 2  BottomInde x  Attacksamples  1  Decaysamples

 1 DI1 Sv / 10
 N i 
Attack  10 log  
10 i 
 AI1 

 1 DI 2 Sv / 10
 N i 
Decay  10 log  
10 i 
 DI1 

Integrals
Three integrals are to be calculated.

MW 1
1
Av 1 
N
10 Sb / 10
BD1
BD1
1
Av 2 
N
10 Sb / 10
MW 2
BD 2
1
Av 3 
N
10 Sb / 10
MW 3

Names: I have called these feature

Av1= MeanSv[MW1..BD1]
Av2= MeanSv[BD1..MW2] return -900 if second bottom does not exist
Av3= MeanSv[BD2..MW3] return -900 if third bottom does not exist

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Secondary features
The following features do not need to be exported, but can be calculated in Excel or any
other spreadsheet directly from the reported points.

Secondary range features

LTM  MW2  BP1
LTMB  MW2  A231
LTTP  B141  BP1
LTA  M W1 - BP1
LPP3  B 231  A231
LPP5  B 451  A451
LPPT  LTMB  LPP

MaxJump.Sv  BP1.Sb  MW2 .Sb

Jump.Sv  BP1.Sb  BF1.Sb

Multi frequency analysis

Multi frequency analysis is described separately in chapter 23_Multi frequency analysis

Data insight

Figure 36. The data insight menu

By data insight we mean ways of looking into the recorded material. Here visualizing is
important and can reveal whether reliable analysis results can be achieved or not. There are
two data sets that can be studied from a split beam echo sounder. The echo intensity
detected by the echo sounders amplitude detector and the phase signal detected by the
phase detector.

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3D-Echogram window
Each time this menu item is selected a new 3D-echogram window will be added to the
existing windows. In a 3D echogram one can study the amplitude and phase information
from selected regions in the ordinary echogram. See chapter 17 for more information.

DIDSON Viewer
The DIDSON Viewer is accessed through the Analysis=>Data insight menu and in the
Analysis => Setup =>DIDSON menu. It is designed to locate and present .ddf data for
regions selected in any echograms independent of what equipment the echogram came
from. Since it is much faster to look through an echogram than to watch through a move,
Sonar5 focus on the echograms, and let the viewer look up and play only selected part of
the echograms. The echogram can be generated from the DISON data or from any other
available echo sounder. Hence, if one observes a target in the echogram and want to take a
closer look at it, selecting that region will cause the Viewer to look up, and play the
DIDSON movie for the selected time / range sequence. The Viewers control dialog
contains tools for controlling the viewer and tools for fish sizing, graphical 2D and 3D
presentations etc.

See chapter 24 Multi beam analysis” for a full overview of the DIDSON implementation.

Oscilloscopes window
Each time this menu item is selected a new Oscilloscope window will be added to the
existing windows. In an Oscilloscope window one can study the echo signal as function of
range, time, along a track or in the frequency domain. Special tools for carrying out
experiments such as analyzing echoes from fish in merry go round and fish swimming
behavior are found in the oscilloscope window. The window is also a useful for studying
bottom sediments and other echo phenomena. See chapter 16 for more information.

Sample data analyzer

The sample data analyzer was originally designed to study why the single echo detector in
the EY500 produced fish tracks with larger ping gaps and more surrounding noise echoes
when the transducer was aligned horizontally in shallow rivers than in vertical open water
situations. The analyzer looks directly into dg files from EY500 containing sample angle
and sample power telegrams. See chapter 18 for more information.

This menu let you add more windows to an analysis such as position diagram windows,
biomass windows etc. In this way Biomass can be combined with tracking or one can study
tracks in many aspects at the same time.

Position window
Position window opens additional position diagram windows (chapter 9). Since each
window can be set up to display tracked echoes from different aspects opening multiple
windows can be a help when studying tracks. Tracking will be enabled as soon as the first
position diagram window is opened.

Echogram window
Sonar5 can handle multiple echogram windows. One echogram can then present the Amp

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echogram while another window presents the SED echogram, another part of the file, a
zoomed part or even a different file, channel or frequency.

Integram window
The Integram window plots the cumulative echo integral for the region selected in the
echogram. This window is frequently applied in ocean work and can help the operator to
see changes in the waters reflection coefficients. This can be useful in order to discover
where plankton start or stop or where fish schools are entering or leaving beam. The
Integram can plot the integral versus ping or versus sailed distance. For the latter, GPS
signal must be available. Distance is convenient when one want to compare Integrams
form different echograms recorded with different ping rates and ship speed.

Cumulative back scattering coefficient sv

The mean sv is estimated for each ping. The first data point in the Integram will then be the
mean sv of the first ping or sailed unit. The next data point will contain the mean value
from the next ping or unit distance plus the mean from the previous and so on.

1 n2
svk   svi
N i n1
Mean sv for one ping k
k
cum _ sv 1..k    sv p Cumulative sv for the kth ping
p 1

Here k indicate the ping number, i is the sample index running through the range layer. n1
and n2 indicates the first and last sample related to the beginning and end of the range layer
and N is N is the total number of samples in the ping (N=n2 - n1).

Cumulative area backscattering coefficient sa

The sa is found from the mean sv by multiplying with the thickness of the range layer.

Rk  Rk ,2  Rk ,1 Height of the analyzed layer at ping k

sa ,k  svk  Rk sa for ping k

k
cum _ sa 1..k    sa p Cumulative sa for the kth ping
p 1

The unit for sa is m2 / m3

Cumulative Nautical area backscattering coefficient sA (NASC)

sAThis is the same as sa except that the unit is 4π18522m2 / m3

Cumulative mean line back scattering coefficient (sL)

The unit for sv is m2/m3. If we multiply sv with an area with unit m2 we get something with
m1 or meter as the unit. It we let the area be the formed by the range and sailed distance in

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the echogram we get the line back scattering coefficient (sL) For a digital echogram we
find this by the following formulas:

xstart  xend
x  Average distance between neighbor pings.
P

Ak  xRk Area between ping k and ping k+1

sLk  Ak  sv k Mean line back scattering coefficient between ping k and ping
k+1

The Cumulative mean line back scattering coefficient is founds by summing up the
individual sl for each ping

k
Cum _ sL 1..k    sL p
p 1

Where lower-case p is a ping index, capital P is the total number of involved pings and
xstart and xstop the start and stop position for the analyzed region in meters. Area is found
from the sailed distance and the thickness of the analyzed range layer.

Frequency response
Sonar5 can analyze all available frequencies. The Frequency response window can be set
up to present the frequency response function, a classification map, differential echogram
or a RGB-echogram. Species identification is one of the aims. Chapter 23 Multi frequency
analysis describes this window.

Track information
Track information opens the track information dialog. See the section Track information
dialog in chapter 9. This dialog presents information about tracked single echo detections.
It has two tabbed pages, one for numerical and one for graphical presentation.

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TS versus range and how to find the layers

Figure 37 TS versus depth for an echogram with distinct size classes at well define layers.
For biomass estimation defining analysis cells is an important task. An analysis cell is
defined by the start and length of the elementary sampling unit (ESU) and by the layer start
and span in the range domain. ESU and Segment is fairly the same thing here. The TS
versus range dialog has been designed to help finding the layers.
How to find the optimal layers
Study the TS distribution at different ranges with the TS versus Range dialog. Note that
changes in TS distribution with range may indicate a change in fish species or age group
composition with range or a bias related to the sampling volume and number of targets.
Compare different regions of the lake (nearshore, offshore). Define range layers for
analysis based on this TS graph. Data should be analyzed in range layers with as
homogeneous fish species and size structure as possible. Different range layers may have
to be used in different parts of the lake. (SOP_Great_Lakes_2008)

Layers are set in combination with the selection of the ESU or segments. The general
recommendation is that each analysis cell should contain
 As homogeneous fish species and size structure as possible
 Enough single echo detections to calculate a reliable average backscattering cross
section

Studying the TS versus range distribution for various regions in the echogram can be a
great help. Not that the selections of segments or ESUs and the number of single echo
detections in each analysis cell will influence on the layer settings. To find the optimal
layers, we recommend using the guided biomass estimation analysis. See the menu:
Analysis=> Analysis=>Guided biomass estimation.

Presenting tracked target features

To present tracked target features, right click, and select “Show selected track feature…”
from the popup menu. Type in the feature number to study, and if the classify window is
present; ensure that the fish basket containing the tracked targets is selected.

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Memo for notes

A memo for noting down the findings is located at the left side of the dialog. A splitter can
reduce and increase the width of this memo. The memo can be used to note down layers
found while studying the TS versus range. The second analysis control dialog can copy the
text and use the noted layers. See the popup menu below.
Popu menu
Right click in the dialog to open the popup menu. The menu contains various options such
as saving and storing layer notes, opening the analysis control dialogs etc.

Figure 38. Popup menu for the TS versus range dialog.

TS distribution and threshold setting

Figure 39, TS distribution presenting data containing detections of Whitefish and Perch
Where to set the thresholds in the acoustic data? This is a frequent asked question. The
TS distribution dialog and the Echmann threshold dialog, described in the next section,
provide two methods for finding the thresholds. This dialog let you study the size
distribution of single echo detections and set all thresholds according to what is learned
from the distribution. The ideal setting will be to find the end of the weak tail of the
distribution for the smallest target of interest and set the start from threshold there. In the
figure above start from threshold has been set to -96 dB and we see three size classes. Next
thing to do is to verify what the classes are by studying the echogram and relate the targets
and depths to knowledge from for example catch data and regressions between species
length and TS. For this example, let us assume that the class from -96 .. -78dB is found to
be false noise based single echo detections, that the three classes between -78..-58, -58..-40
and -40..-24 are target classes of interest, and that the larger echoes comes from bottom

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due to an incorrect bottom line. One should first correct the bottom line until it is seen that
the false bottom noise disappear from the distribution. Then setting the threshold
somewhere between -78 and -80 would be appropriate. In this case it was found that the
noise had started to influence already at minus -70 dB, then one should consider stating
that the size class -78..-58 was infested by noise and could not be analyzed. Hence setting
threshold to – 58 dB would be appropriate. To be able to study the -78..-58 class one
would have to find the reason to the high noise level. Wrong setting of the single echo
detector parameters may be one reason. In that case one can redo the detection. If the
reason is the performance of the echosounder, electric noise, the sea state etc. one may
have to improve the signal to noise ratio and repeat the survey to gain information about
that size class.
Using tracked targets to determine the threshold
The TS distribution dialog works on single echo detections. To study the size distribution
of tracked fish, track the fish, open the fish basket, select option in the fish basket dialog
and check on the histogram. Then click the mean TSc column in the track statistics grid to
present and study the size distribution. If the Mean TSc column is not seen, select it in the
feature library accessed from the fish baskets top menu.

Technical: SonarX has three working thresholds, one threshold for the Amp-echogram,
one for the SED echogram, and one for the biomass estimation size distribution. A full
overview of base, working and warning thresholds are found in chapter 8’s Threshold
section. The TS distribution dialog is designed to help setting the working thresholds in an
easy way and according to the data you have. When studying the TS distribution for a
species, select the Start from value so that it includes the upper and lower tail of the
distribution and do not cut of the weak end. Changing the Start from value in this dialog
will also suggest new values for the Amp and SED working thresholds. Pressing the Apply
button will set up both the SED and Amp threshold in the Echogram control dialog as well
as the Start from, Step, and No. groups in the biomass control dialog.
Popup menu
Help, Chart commander, and the Analyze control dialogs is available from the popup menu
accessed by right mouse click in the TS distribution dialog.

Figure 40. Figure 41. Popup menu for the TS distribution dialog.

Eckmann threshold
This menu opens the Eckmann threshold dialog. The dialog can be useful to find an
optimal threshold for biomass estimation in cases where two different sized species are
present. This is done by plotting average Sv as a function of decreasing threshold. As an
example, assume that one species cover intensities down to -60 dB and another start at -70
dB. Then average Sv versus threshold will increase until -60 dB. Between -60 and -70 dB
it will be stable. When the threshold passes -70 dB, average Sv will start to increase again.
The optimal threshold will then be between -60 and -70dB (Eckmann, R., 1998) .

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Figure 42. Eckmann threshold generated for Kleiner Doellnsee(Ge) (See Demonstration
files / Lakes on the install CD)

How to use
Set the values in the From, To and Step edit boxes. Then select a region in the echogram
with the mouse or with the echogram analyze dialog. Apply the update button if the From,
To or Step values have been changed. This will re-analyze the same area in the echogram
with the new settings. Step can be set to values down to 0.1 dB.

Export data
If the check box “Copy automatically to clip board” is checked, data from the last run will
be found in the clip board from where it can be pasted into alternative software like
spreadsheets.

Other options:
The control bar has buttons for exporting the graph, and changing the view. The use of
these buttons are described in chapter 2 in the section Charts

SED as a function of increasing opening angle

This dialog is opened from the main Analysis => Data insight menu.

The dialog plots the number of single echo detections as a function of distance from the
transducers acoustic axis. The beam is divided into disks starting with a circle or an ellipse
around the axis having an area as defined in the dialogs Area step edit box. All single
echoes located within this inner area are counted for the two size classes defined in the
small and large target panels. The next area is found as a rim surrounding the first area.
This and all other areas are equal in size and the single echo detections are counted for
each of these areas. In the end the number of detection for each area are plotted. X axis
can either be measured in area or gain compensation while the y axis can be cumulative or
absolute depending of the user selections in the Method and X-axis panels.

Two functions, one for small targets and one for large targets can be seen. The purpose of
this dialog is to study the behavior of different single echo detectors such as the Echo

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length and the Crossfilter detector. Questions such as:- Do the detector suppress small
targets in the outer areas more than large targets?, and:- What is the actual beam volume?
- can be answered.

Figure 43. SED versus position in the beam. The dialog is found in the Analysis=>Data
insight menu.
After opening the dialog, select a region in the echogram with the mouse or use the select
region button. A selected region will be remembered and pressing update with different
settings will re-analyze the same region. The large and small target panels enable free
definition of two size classes. If a SED detector based on echo length has been applied, no
detections outside the Max Gain Comp (MGC) will be found. Reconverting the file with a
different MGC setting or using one of the SED detectors in the Analysis => Pre-analysis
menu with higher MGC setting can then enable studies of higher off-axis behavior.

The method starts by looping the opening angle until the beam covers the first area step.
Gain compensation is calculated from the opening angle and all SED detections with
smaller gain compensation factor is counted. The area is then increased with to 2*Area
step. The procedure repeats until the requested gain comp is reached. Independent of the
X-axis selection, all areas will be equally sized and the counting will carried out within
these areas.

Display the actual beam function

An alternative to the Number of SED as a function of increasing opening angle method is
to use the system configuration dialogs erase large targets, set up the system for manual
tracking and with a position diagram in xr-mode and yr-mode. Tracking all available single
echo detections will now reveal the true detection function as a function of range.

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Figure 44. Position window presenting SED positions

In this example we clearly see that there are a difference in the volume of the beam when
only small targets are applied compared with the situation to the right where also larger
targets have been included.

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Main menu

FAST AND EASY CONVERSION WITHOUT ANY FUSS .......................................................................................... 108

WHY DO WE NEED TO CONVERT FILES? ............................................................................................................ 108
Files produced by the converter ................................................................................................................. 108
The converter dialog .................................................................................................................................. 109
Multiple channels ....................................................................................................................................... 109
THE CONVERTERS TOP MENU ........................................................................................................................... 109
File ............................................................................................................................................................. 109
Edit ............................................................................................................................................................. 109
Parameters ................................................................................................................................................. 110
Options menu ............................................................................................................................................. 111
Help ............................................................................................................................................................ 112
THE CONVERTERS STEP 1 SOURCE PAGE .......................................................................................................... 112
? Question button ....................................................................................................................................... 112
1a) - Select echosounder and file format panel .......................................................................................... 112
1b)-Select location and files ....................................................................................................................... 112
1c)- Select options panel ............................................................................................................................ 113
1d)-Set initial parameter panel ................................................................................................................. 114
1e) GPS and disk panel .............................................................................................................................. 114
THE CONVERTERS STEP 2 FILE PAGE ............................................................................................................... 115
2a) Select files button. ................................................................................................................................ 115
2b) Edit initial param. button..................................................................................................................... 115
2c) Generate log button ............................................................................................................................. 115
2d) Save log button .................................................................................................................................... 116
THE CONVERTERS STEP 3 TARGET PAGE .......................................................................................................... 116
File number ................................................................................................................................................ 117
Convert button............................................................................................................................................ 117
Abort button ............................................................................................................................................... 117
MERGING FILES ............................................................................................................................................... 117
APPLYING THE BUILT-IN SINGLE ECHO DETECTOR ........................................................................................... 117
Improving SED by trimming the criteria .................................................................................................... 118
THE SURVEY LOG AND INDIVIDUAL PARAMETER SETTINGS.............................................................................. 118
Sections in the survey log ........................................................................................................................... 120
Free text ..................................................................................................................................................... 120
Sonar parameters and keywords ................................................................................................................ 120
Extracting parameters, annotations and telegram overview from a source file ........................................ 121
PARAMETER TEMPLATE AND LIST OF PARAMETER KEYWORDS ........................................................................ 121
Example 1. Simple survey log .................................................................................................................... 123
Example 2. Survey log with text and keywords .......................................................................................... 123
Example 3 How to take full control of all parameters in a multi channel file............................................ 123
SONAR EQUATIONS .......................................................................................................................................... 124
General equations ...................................................................................................................................... 124
Estimating TS and Sv with the 500 echo sounder series ............................................................................ 129
Estimating TS and Sv in the 60 echo sounder series .................................................................................. 131
Conversion between TS and Sv .................................................................................................................. 134
Converting BioSonics DT4 source files ..................................................................................................... 135
CALIBRATION .................................................................................................................................................. 135
Calibration of single beam systems ............................................................................................................ 138
SOURCE LEVEL (SL) VERSUS ACOUSTIC POWER ............................................................................................... 138

Balk and Lindem 107

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Fast and easy conversion without any fuss

At the converters page named:
 Step 1 Source: Select what you want to do.
 Step 2 Files: Can be scipped*
 Step 3 Source: Press the convert button

This will normally be sufficient. If not, read the rest of the chapter. It is possible to add
additional parameters not found in the echo sounder source files, apply individual file
parameters, descriptions, pictures, survey notes and so on.

* Step 2 can be scipped if one

a) do not want to select a subset of files
b) if one do not need to specify any parameters for any of the files.

Why do we need to convert files?

The converter has three purposes. a) It frees the software from the relation to a particular
echo sounder. b) It converts the data into a format that optimize processing speed c) It
connects echogram data with additional information like survey notes, environmental
descriptions, pictures etc. Figure 45

Initial sonar Recorded sonar file Digital photos,

parameters pictures and sketch
in *.jpg format

Survey log with

notes parameters CONVERTER Converter
and descriptions settings

SonarX project

Figure 45. The converter's input and output flow.

Files produced by the converter

The converter will produce an echogram file containing the Amp and SED echogram. If
depth telegrams have been stored, a file with the extension bottom will be produced. If
navigation telegrams have been recorded, a file with the extension NAV will be produced.
With Sonar5, the operator can select to extract phase information to a file with the
extension Phase. If extracted, this file can later be used to study the phase signal. It also
enables the Crossfilter detector to extract the angular position of the echoes. An overview
of the files produced by the converter is given in the section Files produced by the
converter in chapter 2.

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The converter dialog

The converter dialog is opened from the main menu, File => Converter. It has three tabbed
pages marked Step 1-Source, Step 2-Files and Step 3-Target. Start by setting up the first
page and advance through page 2 and 3. At the second page, four buttons appear. They are
marked with numbers from 1 to 4. It is recommended, but not necessary to press each
button successively when setting up the converter.

Multiple channels
A source files from an echo sounder can contain data from more than one channel. To
enable individual description of each channel, SonarX's converter splits the files. The
converter automatically detects whether multiple channels have been recorded or not. If so,
a message is given and the converter will start to split the original multi-channel files into
new single channel files. Each of the resulting files will be named with the original
filename, but with the channel number added in the extension. As an example
10102305.dg1 will be split into 10102305.dg1_ch01 and 10102305.dg1_ch02 if ch1 and
ch2 was located in the original file. The original file is not altered. When the splitting has
finished, the operator must go back to the converters Step-2 file page, and describe, and
select the newly generated files before restarting the conversion.

The converters top menu

The top menu item contains tool designed to assist at the different converter pages. Items
that do not apply to a specific page will be disabled when that page is selected.

Figure 46. Main converter menu

File
The file menu can save and load the survey log seen at page 2. It can also save the
converter log presented on page 3 and open the file manager designed to delete remove
copy or move source files and converted projects.

Edit
The edit menu has items for handling survey log. Clear all, search, search and replace can
be done here.

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Parameters

Figure 47. The converters parameter menu

NB! The parameter menu contains service routines designed to help the operator with
special tasks. It is not needed for standard conversions.
Initial parameter setting
This menu item opens the initial parameter dialog. The result is the same as pressing button
2-Edit initial parameter. The item is included here too because some users expect to find it
here.
Templates for writing the survey log
This menu opens a dialog designed to help the operator in adding parameters to the survey
log. It is highly recommended to use this template dialog instead of writing the parameters
directly in the log. There are two reasons for this recommendation
a) Using the template dialog will ensure correct spelling of the parameter keyword.
b) The template will always contain the correct set of parameters. This set varies with the
selected converter selected in the main converter dialog's first page. Parameters not
found here will be extracted from the sonar source file and does not need to be
described in the log.

See the section: Using parameter templates in this chapter for more information.
Extract parameters from source file
This menu open the source files found in the selected folder and extract the PE telegrams
found here. If obtained, PE telegrams that apply to SonarX will be inserted in the Survey
log after the correct file name and transect keyword. For everyone working with EY500
EK500 we recommend that the PE telegram is activated in the echo sounders disk menu
and that all parameters found in the transceiver menu are entered while recording the first
file in the field. In addition the SED-parameters and the sound speed parameter should be
entered. In this way one will not have to keep track of these important parameters and one
will not have to add them manually to SonarX's converter. The extraction should be run
after the log has been generated. (Button 3 at the converters second page. During the
search a button for stopping the process will be seen. Pressing the stop button will halt the
process.
Extract parameters from selected, earlier converted .uuu files
This menu extract parameters and text information from earlier converted sonar files to the
survey log. Notes and comments added during the work with the files will be added to the
log as well. The option can be convenient if one want to delete or redo the conversion of a
set of files after having worked with them for a while. The menu item will be enabled
when the filter combo box is set to display converted files (Figure 48). Usage: 1) Select
converted files (.uuu) in the file filter combo box. 2) Select the files to extract information

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from 3) select the menu option. 4) if DG files has been involved, check that the DG file
names written to the log are correct. (Additional text may have been added to the converted
filenames. and the extractor may have difficulties to "guess" the original dg names)

Figure 48. Filter combo-box located in the converters page 2 under the upper left file
listbox.
Add separator line between transects.
If this menu item is checked a line will be added between each file in the log when
pressing button 3-Generate log in page 2.

Parameters->Add default parameters from the parameter setting dialog.

If checked a full set of parameters will be added first in the survey log when pressing
button 3-Generate log in page 2. Parameter values can be edited here and will overrule the
initial parameter settings.

Options menu

Set target folder equal to source folder

Sets the target folder seen on page 3 to the same as the source folder in page 1.

List section
Check on/off menu items that applies to different echo sounders and that will cause the
checked items to be listed in the converter log.

Warning! Listing from many large files may result in tremendous amounts of text and use
up the computer memory. This will slow down the performance and may also result in
instability of the operating system.
Verification
This menu will open a dialog where the operator can set a ping number. Original samples
read directly from file from that ping will be copied to clip board together with the final
parameters for the file. The intention is to ease verification of the converter.

Allow aborting conversion

If checked off, the system will go on and convert all selected files to the end without
checking if the operator has pressed the Abort button.

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Regard Split bam as Single beam

If checked on, the system will remove angle information from the split beam data. This
will make the resulting files equal to files recorded by single beam systems.

Help
Opens this file

The converters Step 1 source page

Figure 49. The step 1 page of the converter. This page deals with selecting the source
folder, selecting eco sounder and setting up thecorrect converter. Note that the panel 1c
will vary according to the selected echosounder.

? Question button
This button gives hints on what to do on this page. Use the top help menu or press F1 to
open this chapter.

1a) - Select echosounder and file format panel

The selector in this panel selects ecosounder/Sonar and source file format.. Press the right
arrow to see a list of available equipment and formatas. When the corrrect equipment and
file format has been selected, the file listbox at the left side of the dialog will show
available files in the folder selected at step 1B.

1b)-Select location and files

Select the drive and folder where the source files are stored. The lower left list-box will
show the available source files in the selected folder for the equipment selected in the 1A
panel.

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1c)- Select options panel

The options will change depending on the echo sounder of file format selected in panel 1a.
Amp echogram panel
This panel controls the extraction of the Amp echogram depending on the choice of
converter. Four possibilities are avaliable at the most. DG.files from EY500 and EK500
can contain precalculated Amp echograms named Echo telegrams in Simrad terminology.
Option 1 extracts this echogram. Passive mode is an option which can be selected if the
DG file contain sample data recorded with the echosounder in passive mode. (transmitting
sound pulses). The two last options can be applied if the echosounder has recorded sample
data. With sample data available SonarX can build up a an Amp echogram with high
resolution. The echogram can be build up contain TS or Sv values.

SED echogram panel

This panel let the operator select wheter the SED echogram should be generated by
applying the built-in single echo detector or by extracting the recorded SED echogram.
(Trace telegram in EY500, EK500 terminology)

Figure 50. SED selector panel located at the converters first page.
Range panel
When the EK60 converter is selected, the 3b panel will change from controlling the SED
echogram to control the range (see Figure 51). The panel enables selection of the layer to
be extracted. The resulting filename will indicate the layer. Layers of until 250m can be
selected down to more than 11000 meters. Selections deeper than available in the source
file will give values below the selected threshold. The converter log written during
conversion will indicate the actual depth registered in the source file. Hence, if one does
not know the registered range, checking the converter log and then re-define the values in
panel 3b may do.

Figure 51. Range panel appearing when Simrads EK60, EY60, ES60 and EA400 raw
format converter is selected.

Extract additional information panel.

This panel contains a checkbox. Checking this box will result in the generation of phase
files with the same names as the original sonar files, but with the extension ".phase". This
file can later be studied in the 3D echogram or used for regeneration of SED echograms by
SonarX's built-in single echo detector or Crossfilter detector. These are located the menu:
Analysis = Pre-analysis menu. Angle information must of course be available in the
source file for this option to work.

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1d)-Set initial parameter panel

The buttons here open the parameter dialog on its different pages. Whether one press one
of the buttons and then select the different tabulated pages in the dialog or press each of the
buttons in the initial parameter panel is the same. Operator should check the pages. The
most important pages are the calibration and the application. Calibration parameters will,
for some echo sounders, be taken from the source file while application parameters are not.
Survey button
Not important. Provides information about the survey
Calibration
Very important, but not needed when parameters are taken from the source files. Ey500
and EK500 do normally not provide any calibration parameters, while other echo sounders
do.
Amp threshold button
This button opens the parameter dialog at the Amp-echogram page. Here the base Amp
echogram threshold can be set. The Amp base threshold defines the lowest possible echo to
be accepted. Setting a low threshold value will
 Increase the ability to detect targets with low echo intensity, and to handle data
with low signal to noise ratio.
 Reduce the systems processing speed because the number of samples to process is
increased.
 Increase the resulting file size.
SED-detector button
This button opens the parameter dialog on the single echo detector page. Here the Single
echo detector parameters can be set.
Application button
Very important. If for example the application is set to horizontal mobile when it actually
was vertical, biomass estimation will apply incorrect equations for things like surface area
and sA. Most parameters here are not provided by the source files from any echo sounders.

1e) GPS and disk panel

The lower panel contains the GPS signal selector and information about the size of the
source disk. In Auto, the selector will select the NMEA string with the highest resolution.
Selecting one of the other available NMEA formats will force the system to extract that
format.

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The converters Step 2 File page

Figure 52. Converter step 2 page dealing with files

NB! This step 2 can be skipped. If skipped, all or selected files at step 1 in the source fiule
list box will be converted. Parameters will be applied as specified in the initial parameter
dialog. In earlier days, when important parameters where not embedded in the source files,
this was an important page. Use this page to select files, specify individual parameters for
different files and apply individual comments and survey field notes. The file list can also
be a help if files has been split into channels and one want to sort on channels to ease
selection of e.g channel 2 files.

2a) Select files button.

Pressing this button will select all files seen in the upper left file list-box. If only a few files
are to be converted, selection can be done directly in the file list box with the mouse.

2b) Edit initial param. button

This button will open the parameter dialog at the calibration page. Hence, It does the same
as the buttons in the Initial parameter panel on the converters first page. If the pages
already have been visited its not necessary to do it again.

2c) Generate log button

Pressing this button will generate a text log in the dialogs right memo window. Only
selected files will be applied. From the top menu's option it is possible to add a listing of
the initial parameters.

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When a log has been generated, it is possible to edit it by adding survey notes for all or
individual files, noting picture names and defining new parameter values for individual
files.

For each file in the log, the initial parameters can be overruled by restating a parameter in
the log. Use the template dialog accessed from the top parameter menu to find the correct
syntax. Notes and free text can also be written in the log globally for all files in the survey
or individually for each file. Global text is written before the first Filename / transects line
and individual texts are given after each filename / transect line. See section "The survey
log” in this chapter for more information about editing a log.

2d) Save log button

If the survey log is saved with the default filename, the survey log will appear
automatically next time the converter is opened. If saved with a different name, it can be
loaded manually from the top file menu.

The converters Step 3 target page

Figure 53. Step-3 target dialog contains selection tools for selecting the destination drive
and folder and buttons to start and stop the conversion.
Target folder is selected with the upper left drive and folder selector. For each folder the
lower left list-box will show earlier converted files. Clicking a file name here will open the
file and show its contents.

The right file list box shows the files selected to be converted. No filenames here indicates
that no files have been selected in the previous page. When a file is converted to its end the
filename will be checked. Only unchecked files will be converted, thus to reconvert a
converted file it has to be checked off.

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File number
This number can freely be set to any positive values before starting the converter. The
number will mark the converted files and will be increased automatically for each file. In
the programs advanced file open menu the number can be presented in addition to the
filename, survey and transect description. Selecting and discussing sonar files in terms of
transect 1, 2 or 3 instead of using the original filenames can in many cases ease the
selection and discussion.

Convert button
Press the Convert button to start conversion. Files not checked in the right list box will be
converted.

Abort button
Press the abort button to halt the conversion. Pressing the abort button during conversion
results in a half converted file. The file will not be checked off in the right file list box but
it will appear in the lower left list-box. From this list-box it can be opened by clicking with
the mouse even if not all pings have been converted. This enables the operator to halt and
check if parameter like the threshold has been correct set without first having to convert
the total file to its end. Repressing the convert button will reconvert the file.

Merging files
Merging files means that two or more files can be connected into one large file. This can
be convenient in various situations. The converter can merge DG files. Later versions of
SonarX can merge converted files as well. Merging converted files is described in chapter
3, section Merging and Re-sampling

To merge dg files, do the following:

a) Select the EK500 or EY500 converter at the converter dialog's source page.
b) Select the files to merge at the converter dialog's file page.
c) Select top menu File => Merge selected files

A new dg file will be generated containing all the telegrams from the selected files. The
new file will be added to the survey log with a list of the appended files. The original files
will not be changed.

Applying the built-in single echo detector

Some echo sounders store the pre made single echo detections in the source file and some
store sample data or both. SonarX’s built in single echo detector can be applied when
sample data are available in the source file. To do so, select the “Apply built-in single echo
detector” at the converters first page as showed on the following figure.

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Figure 54. Selctor panel for the SED source

When the Apply built-in SED is selected, SED parameters must be set in the initial
parameter dialog’s SED page.

An example of settings is:

 Min echo_length = 0.70
 Min echo_length = 1.30
 Max angel std. dev. = 0.3 *
 Max_gain comp = 3 dB
 Mult peak sup. = medium **

* Standard deviation in degrees.

** Use (Off, Medium or Strong)

Note that Max angel std. dev parameter is measured as the true standard deviation of the
mechanical angle samples in degrees. It is not the deviation in the echo sounders internal
electrical phase steps as applied by Simrads Max Phase dev parameter.

Improving SED by trimming the criteria

If "Apply built-in single echo detector" has been selected at the converters first page, the
SED-parameters can be tested and changed.
 Start the converter by pressing the convert button at the converter page 3.
 Press the Abort button after a short period.
 Select the file with the mouse in file list box located at the lower right side of page 3
 Press the panel below the file list box if the echogram do not display the SED
echogram
 Evaluate the echogram. If not satisfied, alter the SED-parameters in the survey log or
by pressing the Edit initial parameter button at the converter's page 2. Then redo this
process.

See section "Single echo detection" in chapter 4 Analyze data to read about single echo
detection and alternative methods to improve the SED.

The survey log and individual parameter settings

Parameters are important. Different echo sounders use different parameters and one and
the same echo sounder may use different parameters depending on the setup and
application. SonarX handles parameters in the following way.
Parameters can be defined in the initial parameter dialog, in the survey log at the
converters second page or in the source files to be converted.
 Survey log: For standard conversions no parameters need to be defined in the

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survey log. However, if one wants to apply field notes pictures or set individual
parameters differently for different files in the same folder, the survey log is the
place to do it. Parameters noted in the survey log has precedence before parameters
set in the initial parameter dialog and before parameters stored in the source files.
 Parameters defined in the initial parameter dialog will be applied unless the
parameter is marked with the “Exist in source file” color or unless it is redefined in
the survey log.
 Parameters located in the source file will be applied only if it is marked with the
“Exist in source file” color in the initial parameter dialog and not mentioned in the
survey log.

Setting initial parameters:

At the converters second page “Step 2 files” page, press the Initial parameter button in the
left panel. This opens the initial parameter dialog. The dialog will tempt to find a useful set
of parameter values for the selected echo sounder, but note that since the source file has
not been read yet, the values within the source file is unavailable. Use the parameter
dialogs file menu to load predefined parameter values, calibration data etc.

Setting parameters for individual files in the survey log:

It is possible to apply individual file parameters and field notes for one or more files in the
log. Individual parameter-settings are written in the survey logs transect sections. The
syntax for this is: parameter keyword = value. As an example Tr_Pulse_Length = 0.1
ms will set the pulse length parameter. The keyword is case insensitive, but must be spelled
correct. The Parameter template dialog opened from the converters top menu “Parameters”
is designed to help the operator adding correct keywords. Only parameters applicable to
the echosounder selected at the Step 1-Source page will be found in the template parameter
list. See the section: Sonar parameters and keywords, and Parameter template and list of
parameter keywords in this chapter.

Note that a parameter statement will be valid from that transect section where it is written
and for all remaining files in the survey log. Note that misspelled parameters will not be
applied and that each misspelled parameter will appear in the comment file accompanying
each converted file together with other survey and transect comments and annotations. The
comment file has the same name as the echogram file, but with txt as the extension.

Overwriting parameters stored in the source file

By default, parameters stored in a source file will overwrite any parameter settings in the
initial parameter dialog if not stated in the survey log. To change this, double click the
parameter in question in the initial parameter dialog or state it in the survey log. The color
will change to indicate that the operator takes control. The operator can now set the value
as he likes. Repeated double clicking at a parameter in the initial parameter dialog will turn
this option off and on.

What is the survey log

The survey log is an ordinary rich text file (survey.rtf) and can describe one or more
surveys. The survey log contains all the information the operator wants to compile into a
set of sonar files. A minimal survey log contains only the source filenames to be converted.

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In addition, the log can describe parameters for individual files and information such as
pictures, text, descriptions, notes, annotations etc.

Tools for writing the survey log

The converter has tools for writing the survey log. Open the converter (File => Converter)
Locate the folder that holds the source files in the converter dialog's page marked "Step 1 -
Source". Then advance to the page marked Step 2-files and press each of buttons marked 1
to 4. This will produce a sufficient log similar to the one seen in Example 1 further down.
If some of the files have been recorded with different parameter settings or if one wants to
attach external information to one or a set of files, this can be done by adding keywords
and plain text as demonstrated in Example 2.

Sections in the survey log

The survey log consists of two kinds of sections. These are the survey section and the
transect sections. A log may have more than one survey sections each followed by many
transect sections. The survey section starts with the keyword Survey and ends with the first
transect. A transect section starts with the file name and the Transect keyword. it ends
before the next transect or survey section. In Example 2 one survey and three transect
sections are described.

Free text
Any free text given in the Survey section, such as the comment about the weather in
Example 2 will be written to all the following transects. Free text, stated in a transect
section, such as the additional weather comment in the third transect section of Example 2
will be applied only to that transect and after the text from the survey section. Free text,
annotation comments extracted from the source files and erroneous spelled keywords will
be stored in a file with the same name as the sonar file but with the extension dot txt. The
information in this file will be presented in the advanced file open dialog (chapter 3) if the
operator points at the file in question. If opened, the information will be available in the
parameter dialog (chapter 10). The main menu: Utility => Parameters open the parameter
dialog. Here the text can be viewed and edited while studying the echogram.

See also the section Text file in chapter 10.

Sonar parameters and keywords

The parameter template dialog described in the end of this chapter can list the available
parameters. For the converter to recognize a parameter in the survey log, each parameter
must have a corresponding keyword. Keywords consist of one word followed by an equal
sign and a value.

Parameters described in the initial parameter setting (opened by button 2 on the converters
second page), and parameters described by keywords in the Survey section of the survey
log describe parameters for all files to be converted. Keywords placed in the transect
sections of the log provides a way to set parameters for individual files.

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If all files in the folder to be converted have the same parameter setting, using the edit
initial parameter button on the converters second page is sufficient.

To add a keyword it is recommended to use the keyword template found in the converters
pull-down parameter menu. This will ensure correct spelling of the keywords. Erroneously
spelled keywords will not be recognized. Instead they will be regarded as free text and
added as notes to the text file generated for the sonar file(s) in question.

The information described by the keywords Survey, operator, Picture and Water Current in
the Survey section in Example 2 will be valid and applied in all the following transects. If a
keyword is redefined in a transect section, the new keyword value will overrule the earlier
values for that transect and for all transects following after.

Erroneous spelled keywords will be regarded as free text as described in the previous
section. The parameter templates can be used to avoid misspelling and to ease the writing
of the log.

Extracting parameters, annotations and telegram overview from a source

file

Figure 55. The converters parameter menu

Some echo sounders can write annotation and parameter setting into the recorded files.
SonarX can extract and add this information to the survey log with the converter dialogs
top menu, Parameters => Extract parameters and info. from source files to all transects
listed in the survey log. The process may take some time if the source files are large. The
log will disappear and an Abort button will be presented while the process is scanning the
source files. Transects will appear step by step with the extracted information added to
each transect section. Pressing the abort button will reinsert the original log with out any
changes.

Note that it is only filenames written in the survey log that count. Selecting files from the
converters upper left file panel does not count.

See section Files, folders telegrams and projects , Telegrams in chapter 2 for information
about telegrams from Simrads 500 series and how SonarX uses them.
.

Parameter template and list of parameter keywords

The purpose for the parameter template is to help the operator writing the parameter
keywords correct. The parameter template can be opened from the converters main menu

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Parameter => Templates for writing the survey log. The menu is active only when the
converters page named “Step 2-files.” are opened. The template sorts the parameters into
categories. Double clicking a line in the template will insert that line in the survey log at
the cursor position. Alternatively, select a line and then press the Apply selected line
button to insert the parameter line at the cursors position in the converters survey log. The
value for the selected parameter is taken from the initial parameter dialog and may have to
be corrected afterwards if the value is incorrect. Remember that the source file has not
been converted yet and that the system cannot know the value unless the operator has set it.

Figure 56. The parameter template dialog is accessed from the top menu's parameter
menu.
Position the cursor in the log where you want to insert a parameter keyword. Open the
templates from the converters top menu and double click at the keyword to insert. As an
example, clicking the SED_Min_Echo_Length in the figure above will insert the following
line at the cursor in the survey log.
;---------------------------------------
02191530.dg2 TRANSECT= Steilene
SED_Min_Echo_Length = 0.80
;---------------------------------------

The value 0.8 is taken from the initial parameter dialog accessed by button 2 "Edit initial
param."

The syntax for a parameter consists of the parameter name followed by an equal sign and a
value. Units are noted as comments and must be separated from the value by at least one
space.

See also the section Importing bottom profiles during conversion and the section importing
water current profiles during conversion in chapter 9.

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Example 1. Simple survey log

;===================== SURVEY =======================
SURVEY = Semsvann
Operator = Balk
Picture = default.jpg

;====================================================
06162341.dg2 TRANSECT= Furnes 1
06172145.dg2 TRANSECT= Furnes 2
06182221.dg2 TRANSECT= Furnes 3

Example 2. Survey log with text and keywords

;===================== SURVEY =======================

SURVEY = River Tana

Operator = Balk
Picture = default.jpg
Water_Current =(22.24,0.54,0.78) (25.20,0.42,0.51) (13.90,0.25,0.29)
It was bad weather with rain and wind during the following recordings
;====================================================
06162341.dg2 TRANSECT= From the west river bank
;-------------------------------------------------------------------------------
06172145.dg2 TRANSECT= From the east bank
Picture = Gillnet.jpg
Tr_TS_Gain = 27.50 dB
;-------------------------------------------------------------------------------
06182221.dg2 TRANSECT= From the east bank
Weather is clearing up
;------------------------------------------------------------------------------------

Example 3 How to take full control of all parameters in a multi channel file
We assume here a complex situation where there is more than one channel in each source
file. The problem may be that one or a few files has wrong parameters the one would like
to correct. The following procedure gives full freedom over all parameters. Step 1-3 referes
to the converters three tabulated pages. Top menu is the converters top menu. Step 1 has
been set up correctly and we start with step-2

1. Step 2: Select source files

2. Step 3: Start the converter and select split files from appearing dialog,
3. Go back to Step 2:
4. Select the top menu Edit=>Sort on channels and select only the split files in the
upper left file selector
5. Press the button named Generate log in the lower left panel. This writes a new
survey log in survey log editor.

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6. Select: Parameter =>Extract parameters and info from source files… , in the
Converters top menu. This read the survey log, and for each source file name,
opens, read, and write the parameters found within the source file to the survey log.
7. Go through the survey log and edit the parameter values.
8. Save the survey log with the button named Save log located in the left panel.
9. Ensure that the correct files are still selected in the upper left file selector
10. Go to step 3 and press the convert button.

Parameters listed in the survey log will overwrite parameters in the source file and
parameters in the initial parameter dialog. If all occurrence of a parameter is deleted from
the survey log that parameter will be taken either from the source file or from the initial
parameter dialog according to the rules stated earlier in this chapter. Hence, full flexibility
and freedom is available.

Sonar equations
General equations
Range
A digital echo sounder store the received power in samples. The distance between a sample
can be measured in range resolution or meter per sample. To find the range of a sample we
simply multiply the sample number with the range resolution.

Eq. 4 r  i  r

r = Range, i = sample index, r=Sample range interval.

Sound freq. (kHz) r (m)

38 0.1
70 0.05
120 0.03
200 0.02
700 0.02
Table 7. Sound frequency versus range resolution in Simrad systems.

Calculating the pulse volume

The echo intensity in the single echo detections are interpreted presented as TS values
calculated by the single target sonar equation. Samples in the Amp echogram are presented
as Sv values interpreted by the volume reverberation sonar equation. To be able to
compare the two, TS values has to be converted into Sv values.
First the wavelength is needed. Wavelength is found from the sound-speed and the sound-
frequency.

 cf
Eq. 5

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 = wave length, f = sound frequency, c = sound speed.

Another important element is the volume of the pulse shell or pulse volume.

dA  r 2 d

A   r 2 d  r 2
0
Eq. 6 c
h
2
c
V  r 2
2
Where r is the range or distance from the transducer,  is the equivalent beam angle, h the
height or thickness of the pulse volume or pulse-shell, c the sound speed and t the duration
of the transmitted sound.

Calculating TS and Sv
Intensity is the power P passing a defined area A. The relation is given by I=PA. The unit
is wm2. The echosounder send an electric signal to the transducer with power Pet. This
power must be converted from electric to acoustic power with a gain factor g. This g
includes both the conversion from electric to acoustic power and the transducer directivity,
and give us the transmitted acoustic power along the acoustic axis:

Eq. 7 pa  pet g

The waves spread out from the transducer in a spherical manner. At the range r from the
transducer, the area of this spherical surface has become A=4πr2, meaning that the intensity
at any point on this sphere has been “thinned” down to I = 1/4πr2. The thinning is called
the geometrical transmission loss. In addition to the geometrical loss, a propagating sound
wave will interact with the water and parts of the energy will convert into heat. This loss is
named alpha (α). Together the geometrical spreading and alpha forms the transmission loss
tl.

1 1
Eq. 8 tl   One way transmission loss
4 r 2 10 r

At the range r we have a target. In sunlight, it would cast a shadow at a wall behind. The
area of the shadow is the area that will be hit by the sound rays in water. We assume that
no energy is consumed by the target so that the incident power equals the reflected power.
We don’t know the target area yet, but name it spherical scattering cross-section (σsp) since
it reflects the sound spherically in all directions. The unit is m2.

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pout  pin
Eq. 9 iout  A1m  iin sp
iout  sp

iin A1m

Solving with respect to σ and gives

iout i i
Eq. 10  sp  A1m   4r02 out  4 out |r0 1
iin iin iin

Target strength TS is defined as 10 times the logarithm to the ratio between the incident
and reflected intensity one meter from the target. Sometimes it is convenient to express TS
by means of σ as well. The intensity ratio can be expressed by sigma as well if we divide
by the reference surface are.

iout i  sp
 sp  4r02  out 
Eq. 11 iin iin 4r02

i   
Eq. 12 TS  10 log  out   10 log  sp2  dB
 iin   4r0 

If we know the TS we can back calculate to find the σ

TS
 sp  4r02  10 10
m2

Where r normally is 1 and omitted.

In many calculations where we want to find the mean TS the 4π is also omitted. This gives
us

TS
4r02  10 10 TS
ts   bs   10 10
which do not have a unit.
4r02

We assume that the intensity from the target is reflected spherically or equally in all
directions, not only back to the echosounder. Therefore, at the echosounder, we have to
divide the power Pout by 4πr2. This gives the echo intensity at the transducer face.

To find the received acoustic power, we multiply with the surface area of the transducer.

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However, since we are interested in the received electric power we mix the area with the
receiving directivity and the acoustic to electric conversion factor g. The electric receiving
area is then

2 g
Eq. 13 ra e  ): electric receiving area of the transducer in unit of (m2)
4
Where λ is the wave length and g the gain due to the transducers directivity properties and
acoustic to electric conversion factor.

The received electric power is found by

pre  pet  tl   sp  tl  ra e

or

 10  r   10  r   2 g 

Eq. 14 pre  pet g   
2 
  sp    
2  

 4 r   4 r   4 

We re-arrange the equation to find the σsp.

1  4 r 2   4 r 2   4 
Eq. 15  sp      pre     r    2  ( unit =m2 )
pet g  10  r   10    g 

In addition to the reflection from a target, we like to define the reflection properties of the
water it self. It is not the water, but the targets in the water that reflects. Since we do not
know the size or number of the targets in the water we say that the sum of hit target cross
section areas  sp reflect the sound. Also this time we assume that the sound is reflected
equally or spherically in all direction as we did with the standard target. Since more water
means more reflecting targets we have to multiply with the actual water volume. Now we
can replace our point target with the water containing an unknown amount of reflectors
 sp  v   sp , and calculate the received power.

 10  r   10  r   2 g 
Eq. 16 pre  pet g     v   sp   
2 

2  

 4 r   4 r   4 

We want to find a reflection coefficient for the water and divide by the water volume.

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Eq. 17 v 
  sp unit = m2/m3=m-1
v
Where the volume v is the pulse volume defined in Eq. 6. We re arrange the equation and
get

1  4 r 2   pre   4 r 2   4 
Eq. 18  v        m-1
pet g  10  r   v   10  r   2 g 

We may call this the Spherical volume scattering cross-section because it describes the
omni-directional reflection of power from a unit “bucket” of water. The volume back
scattering strength Sv or VBS is given by

 
Sv  10 log  v 
 4 

Another way to phrase the equations are:

 p 2 g 2 
TS  Pre  40 log( r )  2 r  10 log t 2ts 

 16 
Eq. 19
 p 2 g sv
2

Sv  Pre  40 log( r )  2 r  10 log t   V (r)

 16
2


Where P=10log(p). An even simpler expression is:

TS  Pre  2TL(r )  Const

Eq. 20
Sv  Pre  2TL(r )  Const  V (r )

Where V(R) is the pulse volume as a function of range. This expression clearly
demonstrates the similarity and difference between Sv and TS.
Since the volume can be rewritten as

 c   c 
Eq. 21 V (r )  10 log r 2   10 log   20 log( r )
 2   2 

, we can subtract range from the transmission loss and the volume to obtain Sv expressed
as a function of TVG rather than a function of transmission loss and pulse volume.

we can define TVG as

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TVG(r ) Sv  20 log( r )  2 r
Eq. 22
TVG(r )TS  40 log( r )  2 r

and we can rewrite Eq. 20 and isolate the constant parts in the end of the equations to find
a computation effective expression for Sv and TS

 c 
Sv  Pre  TVG (r ) Sv  Const  10 log  
Eq. 23  2 
TS  Pre  TVG (r )TS  Const

The full equation to be calculates for each received power at each sampled range bin is
then

  p 2 c  
Sv  Pre  20 log( r )  2r  10 log  T   2Gsv   
  32 2  
   
Eq. 24
  pT 2  

TS  Pre  40 log( r )  2r  10 log    2Gsv 
  16 2  
   

where we have taken out gain and psi from the logarithmic terms since they are given in
logarithmic terms directly by the 500 and 60 echo sounders. Note that all parameters in the
expression inside the parenthesis are constants. Hence they can be calculated one time for
all to save computation power.

Estimating TS and Sv with the 500 echo sounder series

TVG delay in the 500 echo sounder series

Eq. 25 R500  R  (3  r    c / 4)

where R’ is the corrected range (m), R the uncorrected range (m), Δr is the range resolution
(m) or the range occupied by one sample ,  is the transmit pulse duration or pulse length ,
c is the sound speed. Simrad uses c=1500(m/s) here.

Ts and Sv for the 500 echo sounder series

Eq. 26

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  p 2 csv
2
c  
Sv  PR  20 log( R500 )  2R500  10 log t   2G   
  32 2  Sv 
   
  pt 2 cts
2  

TSu  PR  40 log( R500 )  2R500  10 log    2G 
  16 2  TS 
   

Subscript u indicates that TS not have been compensated for off axis position.

Note that this equation differs from the 60 series equation in the correction constants and in
the way the range is estimated.

Single echo target strength TSc for the 500 series

Conversion between electrical and mechanical angles

The various echo sounders store the electric angles and not the mechanical angles in
sample data. To obtain the mechanical angles in degrees the from sample angle data the
following equation is applied.

180 Alo el
Alo mek    Offset Alo
64 Tr _ AngleSensA Lo
Eq. 27
180 Ath el
Ath mek    Offset Ath
64 Tr _ AngleSensA th
Here subscript el and mek. indicates electrical and mechanical angles, Alo and Ath is the
along ship and Athwart ship angle and Tr_AngleSens the electric-mechanical sensitivity
calibration factors and offset the transducer offset angles measured during calibration
procedures. Note that the constants differ from the 60 series described later in this chapter.

Sampling correction for single target detections (500 series only)

The digital echo sounder samples the returned echoes in intervals according to the sample
frequency. One cannot guaranty that the samples hit the actual peak of the echo from a
fish. A parabolic interpolation method does the correction.

ts=10TSu/10

c= is the ts of the peak sample with number i.

a= is the ts of the sample with number i-2.
b= is the ts of the sample with number i-2.
d= is the ts of the sample with number i+1.
e= is the ts of the sample with number i+2.

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(b  d ) 2
ts 
8(2c  b  d )
If 2c  b  d  0.01c
Eq. 28 or c  a  2  ts
or c  e  2  ts
then TSp  10 log( c  ts )
else TSp  10 log( c)
Gain compensation or the off-axis target strength compensation
A fish located in the center of the beam will produce a stronger echo than a fish away from
the center. Since split beam echo sounders provide the off axis positions we can correct for
this with the Gain compensation. (GC)

 Ath 
2
 Alo mek 
2
 Ath mek 
2
 Alo mek 
2
Eq. 29 GC  3 mek      0.18    
 u1   u2   u1   u2  
 

Where GC is the one way gain compensation factor, Athmek and Alomek the targets
mechanical angular positions, and u1 and u2 the half of the -3dB opening angle in the Ath
and Alo directions. This gives the final target strength for a single echo. This gives the
final target strength for a single echo.

Eq. 30 TSC  TSu  2  GC

where c and u indicates compensated and un-compensated target strength.

Estimating TS and Sv in the 60 echo sounder series

Power
Simrad echo sounders store the power as logarithmic based integer values (PRI) in the .raw
file. We find the received power in the following way

P 10 log( 2)
Eq. 31 PR  RI
256

Range in Simrads RAW file format.

The range of a target is found from the relation between the sound speed and the sample
interval.

t
r  c
Eq. 32 2
RTS 60  i  r

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R = Range, c = sound speed, i = sample index, t = sample time interval. r=Sample

range interval. t and c are provided by the raw file recorded by the EK60 echo sounder.
TVG delay in Simrad’s RAW file format.
Simrad’s 60-series apply a TVG delay when Sv is calculated

 c
Eq. 33 Rsv60  RTS 60 
4

No TVG delay are applied in the estimation of TS

Gain and Sa correction in Simrads RAW file format.

SonarX uses two different gain parameters (TS gain and Sv Gain) in the same way as the
500 echosounder series. Since the 60 series operate with one gain and an additional
correction factor for Sv, SonarX has to convert the gain and sa correction into two different
gain factors. TS gain is extracted directly from the raw file while Sv gain is found in the
following way

Eq. 34

10log(g sv2 )  10log( g ts2  sacorr

2
)  20log(g ts )  20log(sa corr )  Gsv  GTS  Sacorr

TS and Sv in Simrads RAW file format.

  p 2 c  
Sv  PR  20 log( Rsv60 )  2Rsv60  10 log T   2G   
  32 2  Sv 
   
Eq. 35
  pT 2  

TSu  PR  40 log( RTS 60 )  2RTS 60  10 log   2G 
  16 2  TS 
   
All symbols have been defined earlier in this chapter.

Single echo target strength TSc in Simrads RAW file format.

Conversion between electrical and mechanical angles
The various echo sounders store the electric angles and not the mechanical angles in
sample data. To obtain the mechanical angles in degrees the from sample angle data the
following equation is applied.

180 Alo el
Alo mek    Alo offset
128 Tr _ AngleSensA Lo
Eq. 36
180 Ath el
Ath mek    Ath offset
128 Tr _ AngleSensA th

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Here subscript el and mek. indicates electrical and mechanical angles, Alo and Ath is the
along ship and Athwart ship angle and Tr_AngleSens the electric-mechanical sensitivity
calibration factors and offset the transducer offset angles measured during calibration
procedures. Note that the constants differ from the 500 series constants

Range and TVG correction

TSu is estimated with a range equal to the range of the individual samples. When an echo
pulse is located as a single target, we have the possibility to estimate the start of the echo
pulse. This is done by first detecting the centre of gravity of the pulse and then subtracting
1/2 of a pulse length. The peak of the pulse gives us the uncompensated target strength
TSu. This TSu is then corrected with a TVG estimated from the new range to form the TSr.

peak gives TSu

start center of
range gravity

Figure 57. Sketching the various aspects of range and TS for a single echo pulse.

 10TSu /10  i 
PulseStop
i

i  PulseStart c
Eq. 37 NewRange  PulseStop

4
 10TSui /10
i  PulseStart
  p 2  
Eq. 38 TSr  PR  40 log( R NewRange )  2R NewRange  10 log T   2GTS 
  16 2  
   
Gain compensation or the off-axis target strength compensation
A fish located in the center of the beam will produce a stronger echo than a fish away from
the center. Since split beam echo sounders provide the off axis positions we can correct for
this with the Gain compensation. (GC)
 Ath 
2
 Alo mek 
2
 Ath mek   Alo mek  
2 2
Eq. 39 GC  3  mek      0.18    
 u1   u   u   u  
 2 1 2

Where GC is the one way gain compensation factor, Athmek and Alomek the targets
mechanical angular positions, and u1 and u2 the half of the -3dB opening angle in the Ath
and Alo directions. This gives the final target strength for a single echo. This gives the
final target strength for a single echo

Eq. 40 TSc  TSr  2  GC

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where c and r indicates total compensated and range corrected target strength.

Conversion between TS and Sv

If an Amp echogram has been stored with 40 log R TVG, biomass estimation methods will
have to convert the TS samples in the Amp echogram into these Sv samples. There are
other situations where we need to convert Sv into TS. Conversion can be done by first
calculating power from the available Sv or TS sample at a certain range. With the range
and power we can calculate what ever we want.

The range of a sample in the amp echogram is given by i  r . Since the different echo
sounders apply different TVG delay functions and different correction factors there will be
different ways to do the conversion. For the 60 sounder series we can convert fro Sv to TS
in the following way

RTS 60  i  r
 c
Rsv 60  i  r 
4
  pT 2 c  
Eq. 41
PR  Sv i  20 log( Rsv 60 )  2Rsv 60  10 log    2Gsv   

 32
2
  
  pT  2  
TSu  PR  40 log( RTS 60 )  2RTS 60 
 10 log  2 
  2GTS 
 
  16  
Converting an Sv sample into a TS sample for the 60 sounder series

For the 500 sounder series we apply the same TVG delay every where and replace RTS60
and RSv60 with R500. In addition the 500 sounder series apples the correction factor named
CSv and CTS.

  c 
R500  i  r    3  r 
 4 
  p 2 c  
Eq. 42 PR  Sv i  20 log( R500 )  2R500  10 log T   2G  2C   
  32 2  sv Sv 
   
  p 2  
TSu  PR  40 log( R500 )  2R500  10 log T   2GTS  2CTS 
  16 2  
   

Converting Sv to TS for the 500 echo sounder series.

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Converting BioSonics DT4 source files

The DT4 files contain run length packed and coded voltage samples. When the voltage
samples are unpacked and decoded Sv and TS are calculated in the following way:

Soundspeed
r 
2  Samplefreq uency
r  MinRange  i  r
TL  40 log( r )  2  Alpha  r

VoltdB  20 log( volt )

c 2  c 
pv ( r )  r  PV ( r )dB  10 log     20 log( r )
2  2 
Sv  VoltdB  2TL  PV ( r )  SL  RS  PRF  CorrSv
TS  VoltdB  2TL  SL  RS  PRF  CorrTS

Where r=range, TL = transmission loss, Corr is a user defined calibration factor, PV is the
pulse volume, Psi is the equivalent opening angle, PRF = Power reduction factor, RS is
Receiver Gain. c=sound speed and tau=transmitted pulse length.

Calibration
The calibration tool is located in the Utilities => calibration menu. SonarX can do an on-
axis calibration. This is not a full calibration and we recommend operators to follow the
calibration procedures and use the calibration software provided by the echo sounder
manufacturer. There are, however, situations where an on axis gain calibration is sufficient,
or situations where one need or want to verify the gain calibration.

Figure 58. Calibration dialog accessed from the Utilities=>tools=> calibration menu.
To use the dialog, set up the SonarX for tracking (Analysis=>Analysis=>Setup=>Tracking
menu) and combine some stable echoes from a target with known TS. (manual or simple
tracking) The track does not need to be stored. Too see the stability of the tracked echoes,
use the Track information dialog found in the Analyse=>Data insight menu and est it up to

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present TS as a function of ping. The target must be positioned in the center of the beam
since this is an on axis calibration. Type the theoretical know TS in the upper left edit box
named Theoretic TS and press the Find new button. SonarX will now use the tracked
echoes to find the mean TS and Sv. These values together with the theoretic TS will be
used to find the new gain and correction factors. The dialogs grid will then report a new
result line with the calibration results and the background figures for the calculations. To
apply the new calibration parameters, select the grid row with the wanted parameters with
the row selector and press the Upgrade now button. If many files need upgrading, it may be
faster to reconvert the files with the new calibration parameters.

Different echo sounders have different calibration parameters. For example- Simrads 60
sounder series use TS gain and Sa correction. Simrads 500 sounder series use Sv gain
instead of Sa correction, while Biosonic sounders use a correction factor. The calibration
dialog will adapt to the sounder that produced the echogram file and present the actual
parameters to be calibrated.

How it works
Set up SonarX for tracking and track part of a stable trace from a standard target. Then
press the find new gain button to see the new on axis calibration parameters. The tracked
part of the target should be on axis. This can be checked in the posigram widow or in the
track information dialog. The posigram is normally presented in the lower right corner of
the program when the system is set up fro tracking. The track information dialog can be
opened by dbl clicking in the posigram window.

What the calibration dialog output

For Simrad 500 series, TS and Sv gain is estimated. For Simrad 60 series TS gain and sA
correction factor is found. For Bisonix, Correction factor is found. In addition the system
estimate theoretical TS and Sv. To give an overview of the background for the estimates
the system output mean TS, Mean Sv, number of echoes, mean range and mean angle
position of the tracked echoes. To find the theoretical Sv gain and sA correction, the pulse
volume parameters, Psi= Equivalent beam angle, c=sound speed, and Tau= transmitted
pulse length are needed. Hence they are also reported for the convenience

The formulas and how it works

If we record echoes from a known standard target, and observe different values when we
post process the echoes, we know that the gain has been set incorrect. With the known and
the observed target strength, and with the known, but wrong gain, we can calculate the
correct gain. We find the correct gain by subtracting the TS sonar equation pair with the
wrong and correct values. This results in a simple equation from where we find the correct
gain.

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  pt 2  
I )TStracked  Pr  40 log( r )  2r  10 log    2GTS ,wrong  2CTS 
  16  
  pt 2  
II )TStheoretic  Pr  40 log( r )  2r  10 log    2GTS ,correct  2CTS 
  16  
Since everything is the same in the two equations except for the TS and the Gain,
subtracting the two equations result in the following simple result.

TStracked  TSTheoretic  2  GTS , wrong  GTS , correct 

Eq. 43 TStracked  TSTheoretic
GTS , correct  GTS , wrong 
2
Where GTS, correct is the gain that will ensure that if applied and if we track the same
detections from the target with a known theoretic TS we will observe that TS for the track.

In addition to the TS gain, Simrad operates with Sv gain or the closely related Sa
correction calibration parameter. These parameters are applied to correct for the echo pulse
smoothed rise and decay. A standard target with known TS placed at a range will produce
an echo that consists of a series of increasing and decreasing sample values. Summing up
Sv for each of these samples for all tracked echo detections and dividing by the summed
number give the mean Sv. This mean Sv should be the same as the theoretical Sv found by
dividing the Theoretical TS with the pulse volume at the target depth. Comparing Sv
obtained from the tracked pulses with the Theoretical Sv let us estimate a new Sv gain in
the same way as we found the TS gain.
 
 10TS / 10   c 
Svtheoretic  10 log   TS  20 logR     10 log 
 c R 2    2 
 2 
G Sv, correct  G Sv, wrong 
Svtracked  Svtheoretic 
Eq. 44
2
Sacorr  GSv  GTS

Where SaCorr is used in Simrads 60 and 400 series and Sv gain is used in the 500 series
Biosonic calibration
Biosonic echo sounders operate with the traditional sonar equations and use a Correction
factor

I TSTracked  VTracked  SL  RS  POW  2TL  Corrwrong

II TSTeoretic  Vtracked  SL  RS  POW  2TL  Corrcorrect

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Where Vtracked= received voltage from the tracked target, SL=Source level, RS=Reseiver
sensitivity, Pow=Power reduction factor, TL the transmission loss and Corr=calibration
factor. All features in the two eq. except for the resulting TS and the Corr are the same,
hence subtracting eq I-II results in a simple expression for the Corr.

TSTracked  TSTheoretic  Corrwrong  Corrcorrect

Rearranging gives the new Corr.

Corrcorrect  TSTheoretic  TSTracked  Corrwrong

Calibration of single beam systems

On axis calibration is possible for single beam systems. The main and crucial point is to
place the standard target on axis. This can be done by trimming the transducer aiming
until the returned echo intensity is as strong as possible.

Source level (SL) versus acoustic power

Source level (SL) is the on axis sound intensity measured one meter from the transducer. It
is common to compare the intensity with a sound pressure of 1 uPascal. Hence we have the
notation SL dB rel. 1uPa at 1m.

Intensity is the power flux or the power floating through each point of a surface. We have
the relationship

Power
Eq. 45 Intensity  with unit W / m 2
Area

Another useful relationship is the relation between the pressure p and the acoustic
impedance of the water z=ρc where ρ is the density of the water and c the sound speed.
p2
Eq. 46 Intensity 
c
If we place the transducer inside a sphere with radius equal to 1m, all the power from the
transducer has to pass through the surface area of that sphere. Thus, the area in question is
A=4πR2 = 4π12 =4π. Since we normally use a directive transducer and since we want the
on axis SL, we must multiply the transducers power with the transducers on axis gain. This
gives

Power  10 Gain / 10
Eq. 47 I tr 
Asurf _ at _ 1 _ meter

and find the source level as

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 Power  10 Gain / 10   Pg 

   
 I tr 
  10 log  surf _ at _21 _ meter   4 
A
SL  10 log     10 log  p 2 
I  p
 ref 
   
Eq. 48  c   c 
 
 P  g  c 
 10 log    10 log( Pg )  170.77
2 
 4  p 

where P is the transmitted acoustic power in watt, g the linear gain, ρc the acoustic
impedance close to 1000x1500 and p the reference pressure being 1 uPascal.

As an example, let P= 300W and Gain=27dB. Then we find

SL = 10*LOG(300*10^(27/10)*1000*1500) - 10*LOG(4*PI()*10^(-12)) = 222.54 dB

where the formula is written in Excel notation and can be pasted to Excel for estimation of
other values.

We can of course also find the Power when we know the Source level.

 P  g  c 
SL  10 log  
 4  p 2 
 

P  g  c
10 SL / 10 
Eq. 49 4  p 2

10 SL / 10 4  p 2
P
10 Gain / 10  c

If we let SL=222.85 dB and Gain=27 we find that

P=( 10^(222.54 / 10) * 4 * Pi() *10^-12 ) / ( 10^(27/10) *1000*1500) =300 Watt

where the formula is written in Excel notation and can be pasted to Excel for estimation of
other values.

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Main menu

ABOUT ...................................................................................................................................................................142
AMP AND SED ECHOGRAM ....................................................................................................................................142
Amp echogram .................................................................................................................................................142
SED echogram .................................................................................................................................................142
Angle echograms ..............................................................................................................................................143
Changing between the Amp and SED echogram ..............................................................................................143
Working thresholds ..........................................................................................................................................143
THE ECHOGRAM MENU ..........................................................................................................................................144
Help ..................................................................................................................................................................144
Echogram control dialog .................................................................................................................................144
Zoom and compress .........................................................................................................................................144
Go to ping menu ...............................................................................................................................................146
Refreshing the echogram..................................................................................................................................146
Layer menu.......................................................................................................................................................146
Bottom menu ....................................................................................................................................................147
Erase unwanted echoes or noise ......................................................................................................................148
Tracking control menu .....................................................................................................................................108
Free hand selection ..........................................................................................................................................108
Mouse tip monitor ............................................................................................................................................108
Event notes* .....................................................................................................................................................109
Integram window..............................................................................................................................................109
TVG menu ........................................................................................................................................................109
Setup.................................................................................................................................................................109
Clone echogram window** ..............................................................................................................................109
Select frequency** ...........................................................................................................................................110
Open other file** .............................................................................................................................................111
Analyze all file ..................................................................................................................................................112
ANALYSIS STARTED WITH THE MOUSE IN THE ECHOGRAM .....................................................................................112
Overruled or rejected analyze requests ...........................................................................................................112
Other ways to start an analysis ........................................................................................................................112
Selecting a region to be analyzed with the mouse ............................................................................................112
BARS .....................................................................................................................................................................113
TROUBLESHOOTING ...............................................................................................................................................114
Why do I not see the echogram ........................................................................................................................114
Why are the echogram colors so strange? .......................................................................................................115

Balk and Lindem 141

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About
The echogram window displays the echogram and let the operator select echoes to be
analyzed. The echogram has two display modes, Amp and SED-mode. Pressing the shift
key toggles between these modes. In Amp mode, the output from the echo-sounders
amplitude detector is presented while the SED-mode presents the single echo detections.
The appearance of the echogram, what pings to be displayed and the selections of echoes
to be analyzed are controlled by the mouse, the keyboard or by the echogram control
dialog.

Amp and SED echogram

Amp echogram
An echo sounder transmits a high frequency carrier signal with frequencies such as 70
kHz, 120 kHz, 200 kHz etc. Echoes are returned with the same frequency. The transducer
receives the echoes with one, (single beam), two, (dual beam) or four (split beam)
channels. An amplitude or envelope detector detects the peaks from the sum of these high
frequency signals. These peaks form a low frequency signal containing the echo intensity.
The low frequency echo intensity is sampled and the samples are interpreted by the sonar
equation and presented as the Amp echogram. The Amp echogram can display the echoes
according to the point source model, the reverberation level model and the passive sonar
equation model. The distance traveled by the sound between two samples is called the
range resolution. The range resolution varies from the different transducer frequencies.

The Amp echogram is important both for tracking and for biomass estimation. When
tracking targets in noisy environments, clusters of false single echo detections occur.
Checking the detections with the Amp echogram easily reveals weather the detections are
noise or origin from a target.

Figure 59. Thresholded Amp echogram

SED echogram
A single echo detector (SED) detects echoes believed to origin from single targets. The
detector evaluates the signal from the amplitude detector and from the phase detector, if
available. With a split beam system, the detections are described with five numbers, (time,

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range, intensity, along-ship and athwart-ship). In the SED echogram the echoes are
presented as points in time and range. The point source model is applied to interpret the
echo intensity.

The SED echogram is important, both for tracking and for biomass estimation. Carrying
out the biomass estimation without knowing anything about the SED detections can be
dangerous. E.g. if there exists noise based detections that do not originates from fish,
which is often the case.

Figure 60. SED echogram

Angle echograms
The echogram can show along ship and athwart ship sample angles. The color scale will
have units of degree relating angles in the echogram to the colors. The angle mode is
useful for fast click counting of upstream migrating fish in rivers. We have also found it
useful for evaluation of the transducer performance. Angle echograms are selected in the
echogram control dialogs Threshold page’s “Echogram disp. mode” selector. ( See the
section Thresholds in chapter 7 ). Sample angles are stored in a separate angle file with the
extension .phase. This file is produced during conversion, but only if the Phase file
checkbox is checked at the converters first page. The Echogram mode selector will indicate
if the file is available or not.

Changing between the Amp and SED echogram

Pressing the shift key toggle between the Amp and SED echogram when the Echogram
window is active. Alternatively the change echogram display mode button in the echogram
control dialog can change between the two echograms.

Working thresholds
The Amp and SED working thresholds are set in the echogram control dialogs Threshold
page. Click the color bar to open this dialog at that page. SonarX operates with base,
working and warning thresholds. To read more about this see the Threshold section in
chapter 8.

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The echogram menu

The echogram menu, seen at the top of the program, call upon the echograms popup menu.
If more than one echogram has been opened, the top echogram menu will open the active
echograms popup menu. An alternative to use the top menu is to right click with the mouse
in the echogram window. Both ways will open the following menu.

Figure 61. Items in the echogram menu

The echogram is controlled by the echogram menu or by the echogram control dialog. The
menu and the dialog interact. The dialog can be accessed from the menu, by pressing the
menu short key F2 or by clicking one of the bars found at the right or bottom of the
echogram.

Help
The help menu opens this chapter.

Echogram control dialog

This menu item opens the echogram control dialog. The dialog interacts with the echogram
menu and controls the appearance of the echogram window. The dialog can also select
regions and start analysis. See chapter 7-Echogram control dialog for more information.

Zoom and compress

Figure 62. The items found in the Echogram = zoom menu

Understanding zooming and compression

Zoom is used when one wants to take a "closer look" at a part of the echogram.
Compression is used to get an overview over larger parts of the echogram. In the horizontal
(time) domain, zooming is achieved by presenting the echoes from each ping more than
one time while compression is achieved by presenting the echoes from every second, third
or fourth ping. In the vertical (range) domain zooming and compression is achieved by

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defining a min. and max range. The echoes between the min and max will be stretched out
to fill echogram window.

The parameters that control zooming and compression are located in the echogram control
dialog described in chapter 7. Parameters controlling horizontal zoom and compression is
seen in the dialog's Horizontal axis page while the parameters controlling the vertical
zooming and compression are located in the echogram control dialogs Vertical axis page.
The ping and range bars in the echogram can be clicked to open the control dialog at the
correct pages. Setting the zoom and compression parameter values directly in the control
dialog is legal and gives a fine control of the echogram.

Compress echogram to show all file menu

When this menu is selected, the total number of ping in the file is divided by the width of
the echogram window. This gives a ratio telling the system the number of pings to skip
between each ping to present. As an example a file with 2700 ping is to be compressed into
a window capable of presenting 730 ping. 2700 / 750 =3.7. The first integer-number
greater than this 3.7 is written to the compress parameter in the echogram control dialog. In
this case Compress=4. Every fourth ping will then be presented on the screen, and the
echogram will be seen to fill nearly the entire echogram window. The operator can set the
compress parameter to any other value to see different compress rates.
Zoom in by drawing a rectangle menu
When this menu item is selected, the mouse cursor changes into the zoom symbol and the
echogram caption explains that the echogram now is in zoom in mode. The program
expects the operator to draw a rectangle around some echoes on the screen. To draw a
rectangle, press the left mouse button down, move the mouse with the button pressed.
Release the button when the rectangle covers the wanted region. The echoes in the
rectangle will now be presented in the entire echogram window and the zoom parameters
in the echogram control dialog s vertical and horizontal page will be updated. The
operation can be repeated to increase the zoom further. Alternatively, the parameters in the
control dialog can be altered manually to achieve the wanted amplification.
Zoom out
If the Zoom in menu has been used, selecting the Zoom out menu will bring the zoom
factor back to the previous zoom level. Two levels are remembered. Pressing Zoom out a
third time will turn the auto range function on. The echogram is then scaled to the total
recorded range.

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Go to ping menu

Figure 63. The Goto ping menu has various menu items for jumping to different ping
positions in the echogram. The same functions are found in the echogram control dialog's
Go to ping page. (See chapter 7)

Refreshing the echogram

Selecting refresh in the echogram menu will refresh the echogram. To achieve optimal
processing speed, the echogram is not automatically updated in all situations. Pressing the
Enter-key (Short key to the refresh menu) forces the system to refresh the echogram.

Layer menu

Figure 64. Two different layers can be defined, a bottom layer that follows the bottom line
and a pelagic layer defined by two parallel lines at constant ranges. Layers are controlled
by the echogram menu and by the echogram control dialog's layer and bottom. See also
the section Layer in chapter 4-Analyzing data.

Layer control dialog

opens the echogram control dialog on the "Layer, bottom and erase" page.

Pelagic layer
turn pelagic layer on /off

Quick define pelagic layer

switches the program into "set pelagic layer" mode. Pressing the left mouse-button down in
the echogram window sets the upper layer line. Moving the mouse without releasing the
mouse button moves the line. Dropping the button drops the layer line at that range.
Repeat the process to position the lower layer line.

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Bottom layer
turn the bottom layer on and off. Note that bottom must have been defined for bottom layer
to work correct.

Bottom menu

Figure 65. Press the right mouse button in the echogram and select Bottom to see the
bottom menu
SonarX provides two different bottom definitions. The first definition is a line restricting
analysis to shorter ranges. This line is normally associated with the bottom seen in vertical
applications. Hence, the line will be referred to as the bottom or bottom line. The second
definition is the bottom profile observed under the beam of a fixed positioned, horizontally
aimed transducer. An over view with references to more information is found in chapter 2's
section: Bottom.
Bottom control dialog
The Echogram => Bottom => Bottom control dialog menu opens the echogram control
dialog on the "Layer and bottom page.
Bottom layer (on /off)
The Echogram => Bottom => Bottom layer menu turns the bottom line on and off the
bottom layer.
Edit bottom directly
The Echogram => Bottom => Edit bottom directly menu will ask the operator to move the
mouse into the echogram and draw the bottom manually by pressing and keeping the left
mouse button down and move it. Different parts of the echogram can be edited. The system
will stay in bottom edit mode until this menu is selected again. When selected the second
time, the operator will be asked whether to save the new bottom or not. If not the change
will be visible until the file is reloaded. Then the original bottom will be seen. The cursor
will be a pointing hand as long as the system is in edit bottom mode.
Bottom on/off
The Echogram => Bottom => Bottom menu turn the bottom line on and off if bottom has
been defined.
Bottom detector and editor
The Echogram => Bottom => Bottom detector and editor menu activates the bottom
detector and edit dialog. The dialog has tools for manually drawing the bottom. It has also
an auto detect and a lost bottom detect function.

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Copy to clipboard
The items in the Echogram=>Bottom =>Copy to clip board menu has been moved to the
Echogram => Export =>Bottom menu. The methods haves been extended to provide
export to clipboard and export to file. The old copy to clipboard menu has been left with a
message about this for older users expecting to find the methods here. See the description
of the Export menu in this chapter for more information about how export bottom data
Save bottom.
Bottom is stored in a separate file with extension ".bottom" Different bottom lines can be
defined and saved for later use.
Load bottom
The Echogram => Bottom => Load bottom menu loads a bottom definition from file.
Why do I not see the bottom line in the echogram?
 The Show bottom line checkbox in the echogram control dialog is not turned on
 The bottom line color is set to the same as the surrounding color
 The thickness of the bottom line is set to a small value so that the line is difficult to see
 The echogram window has been zoomed to show a region where no bottom is defined
 There has not been defined any bottom line, or the file containing the bottom definition
does not exist in the same folder as the echogram file.
 All bottom detection is at 0 meter or at max range

Erase unwanted echoes or noise

See also the Noise section in chapter 4 Analysis

Figure 66.The erase tools are accessed by the Echogram = Erase menu or from the
echogram control dialog's erase noise page.
The eraser tool can remove unwanted echoes. Erased echoes will not be applied in the
analysis. However, no information is lost and all erased echoes can be recalled. An erased
echo is simply an echo that is tagged as erased. Erased echoes are displayed in the
echogram with the color defined for erased echoes in the echogram control dialogs
threshold page. See echogram control dialog (chapter 7). By default this color is the same
as the background color. Hence, erased echoes are invisible. The operator can define any
other color in order to see the erased echoes. Erase and recall can be controlled by the
echogram control dialog. From this dialog one can also select whether to erase both Amp
and SED echoes and only the SED echoes. Erasing SED echoes can be an important task
in situation where erroneous single echo detections have occurred.

Erase control dialog

opens the echogram control dialog on the "Layer, bottom and erase" page.

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Erase unwanted echoes (on/off).

Use this function to remove echoes from the analysis. Pressing E-key when the echogram
window is active brings the program into erase mode. The mouse cursor changes into a
vertical arrow pointing upwards. Moving the mouse with the left mouse button pressed
erase echoes. Pressing the + /- key changes the range that will be erased. Repress the E-
key to turn the echogram back to normal operation. Alternatively press the erase button in
the echogram control dialog's noise panel.
Recall erased echoes.
Use this function to recall erased echoes. Pressing R-key when the echogram window is
active brings the program into recall mode. The mouse cursor changes into a vertical arrow
pointing upwards. Moving the mouse with the left mouse button pressed recalls echoes.
Pressing the + /- key changes the range that will be recalled. Repress the R-key to turn the
echogram back to normal operation. Alternatively press the Recall button in the echogram
control dialog's noise panel.
Recall all
Recalls all erased echoes in the open file. Alternatively press the erase button in the
echogram control dialog's noise panel.
Erase SED in last tracked track.
Tracking unwanted targets and pressing the short key for this menu can be a good way to
get ridge of noise and unwanted targets.
Erase SED in visible layer.
Define a layer and select this menu will remove all SED in the defined layer. This method
can be a good help e.g. to get ridge of stationary targets such as echoes from stones in a
fixed horizontal application.
Export
The export menu can export start a screen grabber, export echogram pictures, sample data,
and bathymetric data to file and clipboard. Select what to export in one of the sub menu
items. When an item has been selected, a dialog will ask whether the prepared data is to be
copied to clipboard or saved to file.

See also the section echogram notes in this chapter for other export options.
Export=>Echogram picture
The Echogram can be exported to other program clipboard or file. Activating the echogram
window and then pressing Ctrl+c copies the entire echogram window. Alternative formats
are found in the echogram menu's Export=>Echogram menu. The color definitions and the
colors of the range and ping bar can be altered to suit any form of presentation. It is also
possible to control whether the echogram should be copied with or without captions and
borders. Sometimes old fish track messages remains blinking. Such markers can be
removed by pressing the c-key. All the needed commands are found in the echogram menu
and in the echogram control dialog.

Without caption
Selecting the echogram menu's Export=>Echogram=>Without caption copies the
echogram window without the caption

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Without borders
Selecting the echogram menu's Export=>Echogram=> Without borders copies the entire
echogram window without the borders.

Export=> Echogram sample data

This export will export sample data, ping, time and GPS positions from the visible part of
the echogram. Since the exported amount of data may be huge, we recommend limiting the
number of pings and range as much as possible. Pings are limited to the visible part of the
echogram. Use the Echogram zoom menu to zoom or set the range and ping zoom in the
echogram control dialogs vertical and horizontal page. Bottom and layer setting in the
echogram control dialogs “Bottom, Layer” page will limit the export further. If the
echogram show data below bottom and the bottom line is on, then the export will not
include data below the bottom line and so on. Data below the applied threshold will be set
to -900 dB. Hence, threshold should be set to wanted value before exporting. Erased data is
set to -901. For large echograms the export may cause tremendous amount of data that can
take long time to export and that may exceed the capacity of many programs like Excel.

Export =>Bathymetric data

The menu option will export bathymetric data for the echogram currently seen in the
echogram window. To export bathymetric data for all or for a selected number of
echograms, use the export menu found in the File=>Advanced file open=>Export menu.
Bathymetric data for all files selected in the advanced open dialog’s file section will be
exported.

Depth, Max Range and relativity

The Utilities=>Parameter=>Application dialog controls the application and the relativity.
THE most important panels here are shown in the figure below.

Depth is exported for vertical applications while Max range is exported for horizontal
applications.

Relativity is controlled by the “Add c to range in the echogram” check box. If checked on,
the value c will be added to the exported depth relative to the surface. If not checked, the
exported depth will be relative to the transducer. The export will indicate this.

Figure 67 Panels in the Utilities=>Parameter=>Application dialog controlling the exort

Margin
Margin set in the echogram control dialogs Layer, Bottom page will not influence on the
exported depth or Max Range. If margin is written to file, then margin will be included in

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the export of depth or Max Range.

Tracking control menu

Figure 68.Tracking control

Tracks can be generated as described in the section "Analysis started with the mouse in the
echogram" in this chapter. Provided that a track has been generated or opened, echoes can
be added or removed.
Add echoes to existing track by use of a rectangle
enable the operator to add more echoes to an existing track by drawing a rectangle around
the additional echoes. Draw a rectangle with the mouse around some echoes. The echoes
will then be combined into a track if the tracker is in manual or simple tracking mode. In
automatic mode the echoes accepted by the tracker parameter setting will be combined. To
add more echoes to the track, press the A-key down and let it up. Then draw a new
rectangle around some other echoes. Instead of generating a new track the selected echoes
will be added to the previous combined echoes. Repeat the process to add more echoes.
The A-key is the short key to this menu item.
Add echoes to existing track by pointing at the echo
enables the operator to add more echoes to an existing track by pointing at the echoes with
the mouse. With the echogram window active, press the P-key. Then move the mouse to
the first echo to add. Press the left mouse button and keep it down. All echoes pointed at
will be added to the existing track until the mouse button is released.
Remove last echo
removes the last echo in the track. Re-pressing removes the next echo.
Draw marker around the new track.
The track will be marked with a blinking rectangle
Draw centerline
enables drawing of a red line trough the tracked echoes for the tracker to indicate the
combined echoes
Remove old markers
remove the blinking rectangle around old tracks
Clear old markers
removes all track markers

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Add track to marked fish-basket*

adds a track to the marked fish basket in the classification window.
Remove last added track from marked fish basket*
removes the last added track from the marked fish-basket. Repressing removes the next
track.
Log track on/off *
Turn the classification window's auto log function on /off.
Show stored track*
Sub menu from where one can select to show First, Next, Previous or Last track in a fish
basket. The short keys Ctrl +Alt+F, N, P or L can be applied to activate to activate the
respective menu items

Free hand selection

Pressing the F-key or selecting the Free hand selection menu will switch to and from
freehand selection. The menu item will be checked and the cursor will show a pencil when
the system is in free hand selection mode. When on, pressing the left mouse button down
and moving the mouse in the echogram window will draw a freehand line. When the
mouse button is released, the line will be closed and information about the selected region
will be sent to all open windows that may want to do something with the selected region.
E.g. the tracker will track and the biomass window will integrate.

Mouse tip monitor

Double clicking the echogram will open the mouse tip monitor and present information
found at the cursors position. The operator can compose the information to be presented by
the checkboxes on feature page. The mouse tip monitor page will present the information
found at the mouse position in the echogram. Moving the mouse will change the
information in this window. Mouse tip logger stores and save information. Double clicking
at a point in the echogram will update the logger for that position. The menu button gives
menu options such as continually log mouse tip etc.

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Figure 69. Mousetip monitor

Event notes*
The event dialog is opened from the Echogram menu =Event.... The dialog enables the
operator to define events. An event consists of a figure and a text describing the event. The
figure can be lines, rectangles or a free hand drawing in different colors and thickness. See
chapter 21 Event notes dialog for more information.

Integram window
This menu item will open an integram window. An integram window plots the cumulative
echo integral in the region selected in the echogram. This window is frequently applied in
ocean work and can help the operator to see where energy starts to enter the echogram or
to separate energy from e.g. plankton and fish.

TVG menu

Figure 70. TVG menu

Each converted file contains a permanent echogram recorded with TVG selected during
original recording. Alternative TVG function can be displayed in order to study the data
(temporary echogram).
Temporary echogram
The changed Amp echogram will be displayed independently of the permanent echogram.
This means that if The Amp echogram intensities of the opened *.uuu file come from Sv
values (20 log R), than TS (40 log R) will be temporarily displayed and vice versa. The
originally selected TVG function for the permanent echogram will still be indicated at the
caption of the echogram window. The temporary echogram is not stored and the echogram
will return to last displayed view upon pressing the Enter key or any other echogram
update functions.
Change TVG
This menu selection produces a new file with changed TVG. The new file will be added a
letter Q in the extension and the original file will not be changed. E.g from MyFile.uuu a
new file named MyFile.uuuq will be generated with the changed TVG. You can easily
switch between the original uuu and the new uuuq by pressing Alt+0 and Alt+1 to switch
between them. If the original file had a 20logR Sv-echogram, the new file will have a

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40logR TSu echogram and vice versa. (TSu =TS uncompensated where uncompensated
means that it is not off-axis corrected as if produced by a single beam system)

What TVG to select?

Selecting 20logR or 40logR TVG influences on the threshold model. Selecting
 40logR TSu echograms gives a threshold model constant to TSu at all ranges.
 20logR Sv echograms gives a threshold model constant to Sv for all ranges.

Constant TSu threshold model (40logR)

With a constant TSu threshold model, a small single fish will be detected equally well at
all ranges. A school of the same sized fish will also be detected at all ranges. As school of
smaller sized fish will only be detected at longer range.

Constant Sv threshold model (20logR)

With a constant Sv threshold model, a small single fish or a small school will only be
detected at short range, while only large schools of this small fish filling the beam will be
detected equally well at all ranges.

Hence, selecting a constant TSu threshold model for the Amp echogram seems most
appropriate for most freshwater biomass estimation work and for tracking and fish
counting.

For macrophyte estimaton or larg schools a constant Sv threshold model seems most
appropriate since the beam normally are filled with targets.

What about the SED echogram if I select a Sv- model for the Amp-echogram?
The SED echogram has only one option and will always have a 40logR threshold model.

Resample*
Opens the resample dialog. This dialog enables changing of TVG, range threshold etc.

Setup
This menu enables the operator to save or load the echogram setup and settings in the
echograms control dialog. Echogram size, position on the screen, selected analysis layers
etc. are stored.

Clone echogram window**

This menu will open a clone of the echogram window. The new window can then be set up
with other display options or it connected to other files, frequencies or channels.

Select frequency**
Use this menu to select what frequency the echogram should present

Open other file**

Different echogram windows can display different files. Use this menu to open another
file.

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Analyze all file

If selected, an analysis all file message will be broadcasted around the system.

Analysis started with the mouse in the echogram

Analysis is done in three steps as described in chapter 4-Analyse data. First the program
must be set up with the correct windows to perform the wanted analysis. Then a region to
be analyzed must be selected and in the end the analysis must be started.
Selecting regions and starting the analysis can be done in one operation by the application
of the mouse in the echogram window. Press the left mouse button down in the echogram
window. Move the mouse diagonally with the mouse button pressed until the appearing
rectangle covers the region to be analyzed. Dropping the mouse button will request all
opened windows to analyze the selected region. If a Biomass window is open, biomass
analysis will be performed. If a position diagram window is open, tracking will be
performed and so on.

Overruled or rejected analyze requests

Operator selection of a region to be analyzed may be overruled or rejected.
 If the selected region is below a visible bottom line the selection will not be analyzed.
Checking off the "Show bottom line" checkbox in the Echogram control dialog will
enable tracking below the defined bottom line.
 Selected ranges will be overruled outside a visible layer when the "Bind analysis to
layer" checkbox in the echogram control dialog is checked. Selecting a region below or
above the layer will be overruled and moved to the layer. If the echogram has been
zoomed so that the layer is not visible, the presentation of the analyzed region will not
be seen.
 If Auto tracking is checked on in the tracker window and the selected regions do not
contain tracks fulfilling the tracking criteria no track will be formed. (Sonar5 only)

Other ways to start an analysis

 From the echograms control dialog's Analyze page (See chapter 07 Echogram control
dialog)
 From the main programs Analysis menu. See section Analysis menu in chapter 02
Getting started
 From the trackers "Start" button. (Sonar5 only. See chapter 12 Tracker)

Selecting a region to be analyzed with the mouse

A region to be analyzed can be selected by drawing a rectangle or by drawing a free hand
selection. Rectangle is the default. Position the mouse at a point in the echogram window,
press the left mouse button down, move the mouse to a different ping and range position,
and release the mouse button to will select a rectangle. To do freehand selections, switch
the system to freehand selection mode by pressing the F-key in the echogram. Press the left
mouse button down and then move the mouse with the left mouse pressed down. Letting
the mouse button up again will close the selection. Selected rectangular and free hand
regions are broadcasted in analysis messages immediately when the mouse button is
released.

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Bars
The echogram window has various bars to inform the operator. These are the caption, the
meter-bar, the time bar, the ping-bar, the status-bar and the color-bar. The bars are selected
and controlled by the echograms control dialog. Selected settings are stored in the set-up
file (SonarX.cfg) and will be remembered to the next time the program is activated. The
color bar is located at the right edge of the echogram window. The caption is the blue line
on the top of the echogram. The caption informs about type of echogram that is showed
and the time, ping and range that the mouse is pointed at. When pressing the left mouse
button down while moving the mouse, the caption will show number of ping and meters
the mouse has been moved.

Troubleshooting
Why do I not see the echogram
1) The echogram window hides behind other windows or it is minimized. Selecting one of
the analysis setup alternatives in the Analysis menu will clear all old windows and
arrange a new set so all windows are visible.

2) The echogram file does not contain echo information. This can happen if the converter
was set up to extract Amp and SED echograms from telegrams not available in the
source file or if the SED parameters were set to values not accepting any echoes. Check
the converter log in the converter's page 3 after a conversion to see a list of available
telegrams in the source file.

3) During conversion, base threshold was set too high so that most or all echo information
was thresholded. Reconvert the file with lower base threshold will do. Base threshold is
controlled from the parameter dialogs Amp page.

4) The user threshold in the echogram control dialog is set to high. Click the echogram
color bar to open the dialog and adjust the threshold.

5) The echogram has been zoomed to present a region without echo information. With the
echogram window active, press the Z-key until the echogram reaches an appropriate
zoom level.

Why are the echogram colors so strange?

The echogram control dialog's threshold page controls the colors. Colors may look strange
if the threshold is set to a strange level or if the color step is set strange. It is common to
operate with a threshold set to avoid the background reverberation and a color step of 3dB
per color for both the SED and the Amp echogram. This is fine for biomass estimation. For
tracking and target studies in situations with low signal to noise ratio, we recommend that
all available information is applied in the Amp echogram. Set the Amp echograms base
threshold to something between -100 and -120dB in the converter and apply the Auto-
threshold and the Auto-step functions in the echogram control dialog. This may give the
echogram a strange look. However, it may be essential for the interpretation of the echoes

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to see the surrounding noise. With Sonar5, all methods based on image analysis works best
when the background reverberation is available.

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Main menu

ABOUT ...................................................................................................................................................................159
MAIN BUTTONS......................................................................................................................................................159
THRESHOLDS .........................................................................................................................................................160
VERTICAL ECHOGRAM AXIS ...................................................................................................................................161
HORIZONTAL ECHOGRAM AXIS ..............................................................................................................................163
MARKERS ..............................................................................................................................................................163
LAYER AND BOTTOM .............................................................................................................................................165
ERASE NOISE PAGE ................................................................................................................................................166
QUALITY PAGE* ....................................................................................................................................................168
GOTO PING OR FILE ................................................................................................................................................170
ANALYZE CONTROL PAGE ......................................................................................................................................171
Ping based analysis ..........................................................................................................................................172
Distance based analysis ...................................................................................................................................173
ANALYSIS CONTROLLER II .....................................................................................................................................175
Analysing single or multiple files .....................................................................................................................142
Controlling the ESU .........................................................................................................................................142
Defining layers .................................................................................................................................................142

About
This dialog can control the appearance of the echogram and it's layers, sets up analysis
regions, start analysis and changes files. The update, help, close and Amp / SED buttons
are common for all the pages. The dialog is accessed from the echogram menu or by
pressing the F2 key when the echogram window is active.

Main buttons
The main buttons are visible at all pages in the dialog.
Apply
Pressing the Apply button will update the echogram according to current settings in the
echogram control dialog.
Apply to all check box
(Sonar5 only). Sonar5 can display many echograms at a time. Each echogram has its own
control dialog. If the apply to all checkbox is checked in a control dialog, then the setting
of that control dialog will be copied to all the other echograms control dialogs and call on
their apply methods as well. If not checked, only the echogram indicated by the control
dialogs caption will be influenced when the apply button is pressed.
Close
Closes the echogram control dialog
Help
Opens this help file.

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Amp / SED
Changes between the Amp and SED echogram. If Amp echogram is presented, pressing
this button will present the SED echogram and vice versa.
Load
Loads an echogram configuration file. The echogram will tempt to present the echogram in
the state it was when the echogram configuration file was saved.
Save
Saves an echogram configuration file with the current echogram viewing parameters such
as window size, threshold and zoomed state.

Thresholds

Figure 71. The threshold page controls the echogram threshold and the color resolution.
Clicking the echogram's color bar opens the control dialog directly on this page.

The "Scroll threshold" scrollbar sets the threshold in the visible echogram. As an example,
if the Amp echogram is presented, the scrollbar will set the Amp echogram threshold only.

See the threshold section in chapter 8 for a full overview of all thresholds in SonarX (Base,
working and warning). The thresholds described here are the working thresholds. See also
the TS distribution dialog described in chapter 4. This dialog is designed to help setting up
all working thresholds.
Threshold-Amp echogram
The Amp working threshold edit box controls the threshold in the Amp echogram. The
lowest possible threshold is the base Amp-threshold set in the converters first page. The
threshold can be raised and lowered, but not below the base threshold. See also section
Setting the thresholds with various TVG in chapter 6.
Threshold- SED echogram
The SED working threshold edit box controls the threshold in the SED echogram. The
lowest possible threshold is the base threshold (min value) set in the parameter dialog’s
SED page during conversion. The threshold can be raised and lowered, but not below the
base threshold. The threshold is applied to echoes compensated for off-axis position. See
section Setting the thresholds with various TVG in chapter 6.
dB per color
Sets the number of dB represented by each step in the echogram's color bar. The bar is

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located at the left side in the echogram.

Base threshold checkbox
Check this box to set the threshold equal to the Base threshold. Base threshold is the
weakest Sv or TS value that was extracted from the original source file during conversion.
Auto step checkbox
Calculates the dB per color from the available number of colors, the defined threshold, and
the strongest echo detected in the file.
Echogram colors
Selectors for color palette, color for echoes below the current threshold, overflow colors,
and mono target color.
Threshold color
Sets the echogram background color. In the Amp echogram this is the color for all echoes
below the threshold. For the SED echogram it is the color surrounding the single echo
detections.
Overflow color
Echoes stronger than the strongest value available in the selected palette will be presented
with the overflow color. The chance for overflow increases especially in the ringing and
bottom zone if dB per color is reduced. The echoes will, however, still have the correct
echo intensity in echo integration. It is just the presentation in the echogram that is
influenced.
Mono target color
When the Mono –Threshold is selected in the palette, all echoes above threshold will be
presented with this color. It can in some situation make tracks and traces easier to see in
the echograms.

Echogram display mode

Amp and SED are normally available. If phase file has been extracted during conversion,
Alo and Ath mode will be awailabel as well. In Alo and Ath mode the colors will represent
the angles and not the echo intensity.

Vertical echogram axis

Figure 72. The Vertical axis page controls the echograms vertical axis and the range bar.
Clicking the range bar in the echogram opens the control dialog on this page.

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Range panel
Defines the start and stop range. The echograms zoom function sets these parameters when
accessed. If auto-range is selected, the values in the "Show from" and "Show to" edit boxes
will be set to the minimum and maximum range detected within the echogram. If the Amp
and SED echogram have been recorded with different range, the values in the "Show from"
and "Show to" edit boxes will change each time the Amp / SED button is pressed. Turn of
the auto range to see the matching echoes at the same position in the two echograms.
Accessing the zoom function in the echogram menu simply sets the "Show from and
"Show to" variables. Setting them manually gives fin zoom control. To be set manually,
the auto range must be checked off.
Flip echogram upside down checkbox
When checked the transducer will be placed on the bottom of the PC monitor looking
upwards (on the screen) instead of on the top of the screen looking downwards (on the
screen).
Auto range check box
If auto range is checked, the echogram will be scaled to the maximum recorded range
independent of what the values in the Show from and Show to edit boxes.
Arrow up/dn key....
The value in this edit box controls the sensitivity of the keyboards arrow up and arrow
down keys. For a value of 10, the echogram will move up or down 1/10 of the height of the
echogram window each time the arrow up or down keys are pressed. Increasing the value
result in finer steps and vice versa.
Edit button and Add to range check box
The edit button will open the parameter dialog at the application page. Here one can
change the information presented in the “Copied info from the application parameter
dialog” panel. If Add to range is checked the value seen in the edit box above this
checkbox will be added to the echograms range and other appropriate places. The title of
the edit box will depend on the application selected in the application parameter dialog.
Range bar panel
Controls the color and visibility of the range bar located at the right side of the echogram.
The Arrow up / down panel
Controls how much the echogram will be moved up or down when the up or down arrow
keys are pressed on the computer.

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Horizontal echogram axis

Figure 73. The horizontal axis page controls the echograms horizontal axis. Clicking on
the echograms horizontal ping or time bar opens the control dialog directly on this page.
The horizontal bar panel
Defines whether the ping, time or status bar should be should be displayed. The color of
the ping and time bar and the interval between the numbers on the bar can also be set here.
Zoom factor panel
Contains two variables, magnify and compress. Magnify defines the number of times each
ping shall be plotted. Compress defines the number of ping to skip between each ping to be
plotted.
The variables are updated when the zoom and compression functions in the echogram
menu are applied.
Advance 1/x page panel
Controls the number of pings the echogram will be moved when the left or right arrow
keys are pressed on the computer. If x=4 and the echogram is displayed from ping 100 to
ping 500, pressing the right arrow key will move the echogram to display echoes from ping
100 +400/4 = 200.

Markers

Figure 74. The marker page.

The marker page defines how the report from an analysis shall be marked in the echogram
window. The tracker reports detected tracks and the Biomass window reports the analyzed
regions. The tracker applies pen 1 when marking a track with a rectangle and pen 2 when

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drawing a centerline. The Biomass window reports non-active sub-regions with pen 1,
while the active sub-region is reported with pen 2. The echogram control dialog's analyze
page defines the number of sub regions.
Markers panel
When an analysis is started, the system broadcast a message about the region to be
analyzed. If the tracker are enabled the tracker will return a fish track message for each
detected track. The track will be reported as described in the track marker panel.
Draw rectangle around tracks (pen 1)
If checked, a blinking rectangle specified by pen 1 will be drawn around a detected track.
Draw a center line (pen 2)
If checked, a line will be drawn through the center of detected tracks to indicate the
connections. The line is not permanent and will disappear if the echogram is updated, e-g
by pressing the enter-key, or if another dialog or window is moved in front of the
echogram for a moment.
Remove old rectangles checkbox
If checked, earlier marks will be removed when a new track has been combined. If not
checked the echogram menus remove marker (shortcut c when the echogram window is
active) will clear all markers.
Clear old button
Pressing the clear old button will remove all old markers and refresh the echogram.
Pressing the short key C when the echogram window is active does the same.
Look up and mark stored tracks
If tracks have been stored in fish baskets the tracks will be marked in the echogram. Only
Selected fish baskets are searched and only tracks from the visible part of the echogram
will be marked. With large fish baskets and files, this function may slowdown the system
performance. If this is a problem, use the Mark once button in stead.
Mark once button
Pressing this button will search through the selected fish baskets and mark tracks found for
the visible part of the echogram.
Pen 1 and Pen 2 panel
This panel contains the description of the marker pens. Set the pen width by editing the
width spin edit boxes set the color by clicking the color buttons and set the style in the
style radio groups. If the pen width is set to a value greater than 1, the style will be solid
for that pen. (Thick pens can not have other styles in Windows 95 and 98).
Number of pixels in each SED detection
A pixel is the smallest element in the computer screen. Plotting individual single echo
detection with one pixel each makes it difficult to see the detections. To increase the
visibility, single echo detections can be plotted by two or more pixels. The upper pixel
indicates the actual echo while the sub sequent pixels below are copies. The "Number of
pixels in each SED detection defines the number of copies. By default this number is set to
3.
Amp echogram update buffer width
This is a technical detail not important to most users. To increase the echogram window's
updating speed, a number of pings are prepared in a buffer before they are copied to the
screen as a complete block. The Amp echogram buffer width defines the number of pings

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to prepare in the block before up-dating the screen. A large buffer results in an uneven but
fast update. A small number results in an even, but slower update.

Layer and bottom

Figure 75. Layer and bottom control dialog.

Show panel
Select layer type.
Surface layer
Set the surface layer line to prevent the analysis to include any echoes from the surface
layer or to include the near field.

Pelagic layer
Controls the pelagic layer when the pelagic layer has been selected. Pelagic layer is
defined by writing the range or depth in the upper and lower edit box before pressing the
update button. Alternatively, press the redefine button and use the mouse in the echogram
to define the bounds. The remaining components define the color and the line thickness for
the presentation of the layer lines echogram.
Bottom panel
Controls the bottom line and bottom layer. Bottom is stored in a separate file. The file has
the same name as the converted sonar file, but the file extension is ".Bottom". If the bottom
file is not found when a converted sonar file is opened, the show bottom line checkbox is
turned off. Tempting to turn it on result in a question asking if the operator want to define a
new bottom line. Answering yes will open the bottom detector dialog. The detector button
can also open this dialog.
The Edit bottom button can be pressed to edit the bottom line manually in the echogram.
Click the button with the mouse and move the mouse to the echogram. In the echogram,
the cursor will show a pointing hand. Press the left mouse button down and move the
mouse to define a new bottom line. Re-click the edit button to escape from the drawing
mode. When re-clicked, a dialog will ask if the newly edited bottom line should be saved.
See the section Bottom detection in chapter 4 and Bottom in chapter 2 for more
information about bottom lines.
The components in the bottom panel have the following functions:

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Show Bottom line checkbox.

Check this box to see the bottom line in the echogram window. If checked, analysis will be
restricted to the range above the bottom.
Line color
Press this button to change the color of the bottom line.
Line thickness edit box
This edit box controls the thickness of the bottom line
Layer
controls the thickness of the bottom layer. To see the layer in the echogram window, the
Bottom layer must be selected in the Show panel, Show bottom line must be checked and
Layer must be different from 0.
Margin
This margin is a temporary margin that changes the depth of the bottom line and bottom
layer. As long as it is set, it will lift or lower the bottom line for all echograms independent
of what survey and transect one opens. The margin is not stored in any echogram bottom
files but only in the SonarX’s configuration file (.cfg). Thus it will be remembered until
next time the system is started. If it is changed, it will influence on the bottom for
echograms opened in the future until it is set to zero.

This margin can be made permanent to a set of echogram files with the “Write margin to
file” button. See description below. Read also about margin in the Bottom detectors
inspector page in chapter 4.

Write margin to file button

This button will write the margin set in the temporary margin edit box to all opened
echogram files. The bottom line in the opened files will then be lifted or lowered as much
as described by the temporary margin. To avoid confusion, the temporary margin value
will be set to zero. Hence, the result will be a bottom line seen at the same depth as before
but this line will now be permanent. Adding a constant to the detected bottom line can also
be done with the margin button in the Bottom detector (chapter 4).
.

Erase noise page

Figure 76. Erase noise dialog page

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Erased data is the same as no-data. Echoes in the SED and Amp-echogram can be erased
and recalled manually and automatically. Erased echoes are marked as erased. They are
always present in the echogram, but will be presented with the color set in the option panel.
When this color is the same as the background color, erased echoes will not be visible.
Erased echoes are excluded from all analysis. The will not add to biomass and can not be
tracked.

In addition to be marked as erased, echoes can also be marked with a quality stamp. It is
possible to erase high or low quality echoes in the quality page.

The methods on this page can also be controlled from the echogram’s erase menu. See the
echogram => erase menu to find convenient short keys. Erasing and recalling echoes are
further described in chapter 6's section: Erase unwanted echoes.

Recall all button

Pressing the Recall all button or pressing the T-key when the echogram is active will recall
all erased echoes in an open echogram file
Recall button
Pressing the Recall button or pressing the R-key when the echogram is active will enable
recalling of selected echoes. When pressed down, this button will stay down until it is
repressed or until the R-key is repressed in the echogram. When this button is down, the
mouse cursor will show an arrow if the mouse is moved to the echogram. Pressing left
mouse button down and moving the mouse will recall erased echoes. Echoes will be
recalled from the tip of the arrow and down to as many samples as indicated by the eraser /
Recaller size edit box. Recalling a selection can be needed if one e.g. have erased too
much.
Eraser button
Press this button to turn the echogram into erase mode. Move the mouse to the echogram
and see the cursor change to an arrow up. Press the left mouse button down and move the
mouse to erase echoes. A red band will tail the cursor to indicate what has been erased. Let
the mouse button up to end the erasing. The echogram will now update and present the
erased echoes with the color selected with the color button in the in noise eraser panel. If
the Only SED checkbox has been checked, the echogram must be in SED-display mode to
see any changes.
To turn of the erase mode, re-click the erase button, press the recall button, or press the E-
key when the echogram window is active.
Invert button
The Erased tag will be set on all echoes or samples that do not have an erase tag and vice
versa. For example, if fish traces have been marked as erased in a file in order to study
plankton, pressing the Invert button will hide the plankton and show the fish.
Erase or recall only SED, not Amp checkbox
If checked, erasing and recalling will only operate on the SED echogram and not the Amp
echogram.
Erased echo color button
By default erased echoes are colored with the same color as the echogram background.

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Click the button to open the color selector. Changing the color for erased echoes to
something different than the background will display the erased echoes. They will still be
regarded as erased by the system but the operator will see what is erased.
Erase / Recall size edit box
defines the range to be erased when the mouse is used to erase echoes
Erase SED in last tracked track.
Tracking unwanted targets and pressing the short key for this menu can be a good way to
get ridge of noise and unwanted targets.
Erase SED in visible layer.
Define a layer and select this menu will remove all SED in the defined layer. This method
can be a good help e.g. to get ridge of stationary targets such as echoes from stones in a
fixed horizontal application.

Quality page*

Figure 77. Quality page set up to redefine the quality.

Single echo detections can be marked with high or low quality. If the detection fulfills the
setting in the SED quality definition page, it is defined as a high quality echo. If not it is
marked as a low quality echo. Echoes are marked with quality when one of the detectors in
the Analysis => Pre-analysis menu is applied. Quality is not defined when the built in SED
detector are applied in the converter. Quality can, however, be redefined with the tools
located in the Quality / Redefine quality page.

The main idea with the quality concept is to allow SED with strict and loose definition at
the same time. For tracking it is important with well detected tracks without ping gaps. For
size, position, velocity and abundance estimation high quality is important. If the quality
concept is used, the system can use all echoes in the tracking and only high quality echoes
for analysis methods sensitive to quality.

Echoes with low or high quality can be erase and recalled.

SED quality definition

This panel holds a set of single echo criteria. See description of the parameters for the echo
length detector for more information about the individual parameters. Echoes within the

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description will be defined to have high quality if the redefine button is pressed.
Show quality in file / default
Pressing the “in file” button will set up the quality definition as it has been defined in the
open echogram file.
Pressing the default button will set up the quality definition page according to default
values.
None of these buttons will alter the quality in the file. To alter, Redefine 1 or 2 have to be
pressed.
Do not apply low quality echoes in analysis
Redefine 1
This button will take the current definition seen in the quality definition panel and test each
existing SED in the open file against this definition. Echoes fulfilling the requirements will
be marked with a high quality mark and vice versa.
The method works best when the Amp echogram contains high resolution data (many
samples per meter). To be able to detect parameters such as max phase deviation max gain
compensation, the .phase file must be available. If not, the system will only apply min
target size and echo length in the redetection of the quality. Phase file is extracted during
the conversion if the Extract phase file checkbox is checked. The box is located on the
converter first page.
Redefine 2
Same as above, but will redefine quality in all files selected in the file open dialogs.
Update quality in tracked targets
Tracked and stored targets consist of copies of the SED that was connected in the tracking.
These echoes will be marked according to the quality defined when the target was tracked.
If the operator later redefines the quality in the echogram, targets tracked before the
redefinition will be marked according to the previous definition. The update button enables
the operator to update the quality in tracked targets according to the current quality defined
in the echogram. All tracks in all fish baskets seen in the Classify window will be updated.

Figure 78. Quality page set up to erase or recall echoes according to the quality definition
The erase by quality page can erase echoes according to the quality marks defined for each
echoes or according to the definition in the SED quality page. This makes it possible to
erase echoes according to quality without altering the actual quality stamp set on the SED.
Erased echoes can be recalled by the upper left Recall all button. To recall local regions,
switch to the noise page and use the Recall button.

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Erase 1
All existing SED with SED criteria outside the criteria set in the SED quality definition
panel will be erased. If the Echo length is set to 0.8.. 1.2 as in the example above, echoes
with echo length less or greater will be erased. To be able to erase echoes according to the
phase based criteria, the phase file must be available.
Erase 2
This erase method applies the current quality marks stored with each SED in the SED
echogram. The parameters seen in the SED quality definition panel is not applied, but
pressing the “in file” button below this panel will show the setting that caused the quality
marks. Phase file is not needed for this operation.
Apply the following to □ SED □ Amp echogram
If SED is checked the Invert and Erase buttons below this line will work on the SED
echogram
If Amp is checked the Invert and Erase buttons below this line will work on the Amp
echogram
Invert button
This button will erase all visible echoes in the echogram and at the same time recall all
earlier erased echoes. The method will be applied to the echograms checked in the “Apply
the following to...” check boxes.
Erase if TS is greater than the defined Min target size
This button will erase all echoes with TS greater than defined by the min target size
parameter in the SED quality definition panel. Since threshold takes away echoes with
lower TS than the threshold, a button for this operation is not needed. The method will be
applied to the echograms checked in the “Apply the following to...” check boxes.

Goto ping or file

Figure 79. The Goto page assists the operator in moving around in the echograms.
Looking through a set of echogram files
The best way to look though a set of echogram files is to select and open all the files with
the main File open or File open advanced menu, and then use the PgDn, PgUp, Arrow left,
and arrow right keys on the keyboard. When reaching the end of one file the echogram
will jump to the beginning of the next file according to the setup in the Behavior panel. If
moving towards and reaching the beginning of a file, the system will open the previous file

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also according to the setting in the Behavior panel. The Home, End, Prev file, Next file,
and Page buttons will do the same as the respective hort keys: Ctrl+Home, Ctrl+End,
Alt+P, Alt+N, PgDn, PgUp and arrow keys.

Showing echogram from…

To display the echogram from a selected time or ping number, the scrollbar can be moved
until the correct time or ping are displayed. A ping number can also be written directly in
the center edit box.

Page divisor
This edit box defines how much the arrow keys shall move the echogram. In the figure
above, the box is set to 4, meaning that the echogram page will shift with ¼ of the visible
page. If this is changed to 2, the buttons marked ¼ page will change to ½ page. This will
also influence on the keyboards arrow keys.

Behavior panel
This panel controls what will happen at the beginning and end of a file. If the system is set
up to ask the user, then a question dialog will appear at the beginning and end of a file.
The question dialog has a button that will bring the operator directly to the echogram
control dialog’s Goto page. Coming this way will show the Behavior panel in green to
indicate what to do. Normally the panel will have same color as the other panels.

The first row of buttons provide an alternative way of "moving around" in the echogram,
while the lower row of buttons can jump between the different files earlier selected by the
file open menu. As an example, if file number 1, 3, 4 and 7 has been selected in the file
open menu and file 1 is displayed in the echogram, pressing the "Next file" button will
open file number 3. Repeated press on this button will open file number 4 and then number
7.
Replay panel
Pressing the play button will start scrolling the echogram over the screen as if it was a real
time recording. Pause will stop and rewind will move the echogram back to where replay
was started. Ping per sec will be correct only if the computer is able to keep up with the
requested speed. The function can be used to locate a certain event. It can also be applied
for demonstration purpose. Dr. Marc Schmidt requested this method in January 2007.

Analyze control page

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Figure 80. The Analyze page assists the operator in defining a region to analyse.
The blue hyperlink in the upper right part will open the Analysis II control dialog. See next
section.

Ping based analysis

From ping
Defines the start ping of a region to be analyzed. Pressing the From page, Visible page or
All file buttons will update this edit box. If the "Update region with the mouse" is checked,
From ping will be set when a rectangle is drawn in the echogram. From ping can also be
set by moving the From ping scroll bar.
# Ping
Defines the number of pings to be analyzed. Pressing the Visible page or All file buttons
will update this edit box. If the "Update region with the mouse" is checked, # Ping will be
set when a rectangle is drawn in the echogram.
To ping
Defines the end ping of a region to be analyzed. Pressing the From page, Visible page or
All file buttons will update this edit box. If the "Update region with the mouse" is checked,
To ping will be set when a rectangle is drawn in the echogram. To ping is can also be set
by moving the From ping scroll bar. Toping will then follow #ping after From ping.
Setting the To ping will update # ping and vice versa.

From range
Defines the start range of a region to be analyzed. Pressing the Pelagic layer or Max Range
buttons will update this edit box. If the "Update region with the mouse" is checked, From
range will be set when a rectangle is drawn in the echogram. From range can also be set by
moving the From range scroll bar.
# Meters
Defines the number of meters to be analyzed. Pressing the Pelagic layer or Max Range
buttons will update this edit box. If the "Update region with the mouse" is checked, From
range will be set when a rectangle is drawn in the echogram.
To range
Defines the end range of a region to be analyzed. Pressing the Pelagic layer or Max Range
buttons will update this edit box. If the "Update region with the mouse" is checked, To

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range will be set when a rectangle is drawn in the echogram. To range can also be set by
moving the From range scroll bar. It will then follow # meters under the From range.
Setting the From range directly will update the # meters and vice versa

Sub segments
Defines the number of segments the region should be divided into when performing
biamass analysis.
Sub layers
Defines the number of sub-layers the region should be divided into when performing
biomass analysis. When analyzing bottom layers, this value will automatically be set to 1.
From ping scroll bar
Moving the From ping scrollbar will move the region to be analyzed in time, update the
From ping edit box and perform an analysis at the new ping position.
From range scroll bar
Moving the From range scrollbar will move the region to be analyzed in range, update the
From range edit box and perform an analysis at the new range position.
Update region with the mouse
If the Update region with the mouse is checked, the From ping, From range, # Ping and #
Range edit boxes will be set according to the rectangle drawn with the mouse in the
echogram.
Set ping to and Set range to buttons
Pressing these buttons will update, the From ping, From range, To ping, To range, # ping
and # meter edit boxes according the applied button. A message will appear and tell what
will happen. Pressing ok to this message will update the edit boxes, but no analysis will be
carried out before the operator presses the Analyze button.

Auto exports
The auto export panel and its setup button let you select additional exports. The setup
button will open the system configuration dialog on the general page. Here a suite of
exports can be selected. The status indicator will turn green if any exports are selected.
Read more about Auto exports in chapter 11’s, general section.

Distance based analysis

Analysis based on

Figure 81. The Analysis based on radio group.

This radio group located at the right side of the Analyze page contains two choices, ping
and distance, Ping is the default and works as described above, Distance will exchange the
items in the lower part of the analyze page with a distance panel. Here the operator can set
a distance such as 1852 meters. Pressing the test button will calculate start position at From
ping, and set the # ping and To ping closest to the given distance from the position selected
by the From ping. If sub segment is set to a value higher than 1, the system will divide the

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selected distance into equal sub distances and base the analysis on this distances. The
number of ping in each analyzed segment may then vary depending on the ship velocity. In
the Biomass window's result grid, both involved pings and distances will be seen when the
analysis is based on distances. Note that it is the exact ship trajectory that is applied in the
calculations. Note also that there will be uncertainties in the distances related to the
accuracy of the navigation system, the frequency of position registrations applied in
transects. Linear interpolation and extrapolation is applied to relate pings and positions if
no position is registered at the time of the ping.

Figure 82. This panel will appear if the analysis based on distance is selected. The
distance is given in meters. A multiplier and a label are applied to ease conversion
between meters and Nautical miles (NM)

Distance and multiplier edit boxes

Note the distance to be analyzed in this edit box. Distance is set in meters. To ease use of
nautical miles, set the distance to 1852 and the multiplier to the number of NM to be
analyzed.
Test button
Pressing the test button will test whether the applied requested distance can be analyzed or
whether it exceeds the file.
Set max dist. button
This button finds the distance between the first and last ping. From ping is set to 1 and To
ping is set to the last ping.
Divide file in button
Sets the segments and distance from the value in the From ping to the end of the file to
obtain as many equal segments to analyze as possible.

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Analysis controller II

The Analysis II controller has been designed to solve analysis tasks that the analysis I
controller can not handle, such as multi file operation, variable layer size and various ESU
units.

Options
 Allocate ESU’s for entire files or between start stop events defined in the
echograms
 Let ESU cross file border
 ESU units can be ping, meter, or minutes.
 Accept a user defined jitter or (variable ESU size) for the last ESU
 Free definition of multiple layers
 Layers can be bottom or surface related or related to percentages between bottom
and surface.

Analysing single or multiple files

If the Current file selector is checked, only echogram seen in the echogram window will be
analysed. This is independent of weather one or many files has been selected in the file
open dialog. To analyse multiple files do:
a) Select all the files to be analysed. This can be done directly in any of the file open
dialogs. Files can also be selected directly by pressing the controllers Menu button.
b) Check the All selected checkbox

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c) Press the Analyse button

The system will now process all the selected files according to the setup in the analysis
controller II and according the specified analysis. If the system is set up for tracking, all
specified layers in the selected files will be tracked. If the system is set up for biomass
estimation, all defined analysis cells in all selected files will be analysed, and the result
will be stored in the biomass basket.

Controlling the ESU

ESU is short for elementary sampling unit. It can be ping, distance or time based. Select
length and unit in the ESU panel’s upper length edit box and unit selector. The start stop
panel controls how the ESU’s are to be applied to the echogram files.

Start and stop panel

The start stop panel describes the relationship between the ESUs and the echogram files.
They can be distributed between file start and stop or between start and stop events.
Entire files selected
When selected, the system will split up the selected files in ESUs from the beginning of the
first file to the end of the last file.
Events in echogram selected
When selected, the system will start the analysis, not at the beginning of the first selected
file, but at the first Start event. ESUs will only be defined between start and stop events set
in the echograms. When selected, the system will regard the events instead of the files.
Between a start and stop event, there can be one or many analysis cells. See “How to set
ESU…” later in this section below for how to let the start and stop event define the entire
ESU

Edit button (only visible when needed)

This button appears behind the Events in echogram selector when it is selected. Press the
edit button to open the event editor prepared for setting start stop events in the echograms.
See chapter 21, section Analysis start and stop events for more information.
Accepted jitter % edit box
The end of the last ESU may pass an "end of file" or a "stop" event. If jitter is set to e.g.
10%, the jitter will enable the last ESU to be accepted if it is up to 10% shorter than the
required ESU.
If it is shorter than allowed by the jitter, it will be excluded

How to set ESU’s equal to Event start - stop pairs in the echogram?
The distance between a start – stop event pair in the echogram can either be divided into a
series of ESU’s, or an ESU can be set to last through the entire event start – stop length. To
get ESU’s that fill the entire interval between start – stop event pairs, do this:
a) Sett the ESU length to a value that guaranteed will be longer than the longest event
interval.
b) Set the Accepted Jitter to 100%

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Let ESU cross file borders

If checked, the system will let the ESU’s cross from one file into the next in order to get
sufficiently long ESU’s . For example, if the ESU is supposed to be 500 meter long and
there is only 100 meter left in the file wher it starts, 400 meter will be taken from the next
file. If that file only contain 300 meter, the last 100 meter will be taken from the third file.
If there is no third file selected, the jitter control will evaluate whether to accept or discard
this ESU.
How crossing file borders works
Whenever an ESU want to cross file border, a new echogram file is generated for that
particular ESU. The first ping in that file will contain the echoes from where the ESU start.
Pings are picked from successive files until the ESUs requirement are fulfilled according to
nr of pings , distance or time.
Cleanup crossing files checkbox (only visible when needed)
If checked, temporary files containing date for ESU’s that are picked from the involved
echogram files will be deleted as soon as they have been used. If you want to study these
files, uncheck the Cleanup check box and open them in with the file open menu after the
analysis has been run.

Defining layers
The layer panel consists of a layer option selector, a layer end definition selector, and a
layer memo box.
Layer selector
There are three options available, a) From transducer, b) From bottom, and c) Percentage
of transducer – bottom.
The text will vary depending on the transducer mounting selected in the Parameter dialogs
application page. (See the utility menu).
Layer stop definition selector
Layers in the layer memo consist of rows with two numbers. Each row specifies one layer.
The first value on a row specifies the layers start range. The second value specifies either
the thickness of the layer or the stop range. The meaning is defined by the “Layer stop
definition selector”
Layer memo
The layer memo holds the layer start and stop or thickness values. One row for each layer,
starting with the
layer start depth, followed by the stop or thickness. A row starting with a semi-column are
regarded as a comment.

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Figure 83. Analysis controller II ‘s layer panel. Left set up with three layers using the
From, To definition. Right: Same layers, but now defined with the From, Thickness
definition. Both situations will result in the same layers being analyzed.

Making layers automatically

The menu button holds two methods for written layers into the memo. The layer generator
can fill up the memo automatically. The TS versus range dialog let you study the target
strength distribution as a function of range, to help defining appropriate layers. See the
section;- TS versus range in chapter 4.

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Main menu

ABOUT ............................................................................................................................................................. 180

PERFORMING A BIOMASS ANALYSIS ................................................................................................................ 181
UNDERSTAND THE USE OF THE AMP AND SED ECHOGRAM ............................................................................. 181
THE ITEMS IN THE BIOMASS WINDOW .............................................................................................................. 182
Region grid (RG) ........................................................................................................................................ 182
Size Group Chart (SGC) ............................................................................................................................ 182
Size Group Grid (SGG) .............................................................................................................................. 182
THE POPUP MENU ............................................................................................................................................. 182
CORRECT SONAR PARAMETERS ARE IMPORTANT ............................................................................................. 185
THRESHOLDS ................................................................................................................................................... 185
Two Base thresholds .................................................................................................................................. 186
Three Working thresholds .......................................................................................................................... 186
An easy way to set all the working thresholds............................................................................................ 187
Warning thresholds .................................................................................................................................... 187
BIOMASS CONTROL DIALOG ............................................................................................................................. 189
Species Id selector ...................................................................................................................................... 192
RESULT OUTPUT .............................................................................................................................................. 193
Biomass window output.............................................................................................................................. 193
Biomass basket ........................................................................................................................................... 194
The items in the Biomass basket ................................................................................................................. 197
Export......................................................................................................................................................... 198
SCALING THE ACOUSTIC RESULTS TO DIFFERENT FISH SPECIES ........................................................................ 198
BIOMASS ESTIMATION BASED ON TRACKED FISH ............................................................................................. 198
HORIZONTAL SURVEYING ................................................................................................................................ 199
FISH LENGTH AND WEIGHT ESTIMATION .......................................................................................................... 200
ASPECT CORRECTION ....................................................................................................................................... 201
TROUBLE SHOOTING ........................................................................................................................................ 203
CALCULATIONS ............................................................................................................................................... 204
AREA DENSITY ................................................................................................................................................. 205
Area density for vertical applications ........................................................................................................ 206
THE FOUR BIOMASS ESTIMATION METHODS ..................................................................................................... 206
Biomass estimation based on sv /ts scaling ................................................................................................ 207
Biomass estimation based echo counting ................................................................................................... 209
Biomass estimation based on the trace counting method ........................................................................... 210
Biomass estimation based on tracks and catch data. ................................................................................. 212
VERTICAL VERSUS HORIZONTAL BEAMING ...................................................................................................... 212
BEAM HEIGHT, VOLUME AND AREA ................................................................................................................. 213
PARAMETERS INVOLVED IN THE BIOMASS CALCULATIONS .............................................................................. 223
BIOMASS ESTIMATION BASED ON SV / TS SCALING, A CALCULATION EXAMPLE ............................................... 224

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About
For vertical mobile applications we recommend to use the SGA.

The SGA (Software guided Analysis) is located in the Analysis menu at the top of the
program. It will guide you through all important steps from survey planning to the final
analysis report. During the analysis, the Biomass window is a key window.

The Biomass window performs abundance estimation. With the aid of the species data
base, abundance are converted to biomass. With the aid of the catch basket, biomass can be
scaled into species. For Sonar5, all described methods are available. Sonar4 are designed
for abundance estimation and for vertical applications.

Figure 84. Echogram window indicating the analyzed regions. The biomass results
presented at the moment are marked red while the remaining regions that have been
analyzed are indicated with black lines. The yellow line is the bottom line. Line colors,
thickness and style are user defined.

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Figure 85. Biomass window’s analyze page.

Performing a Biomass analysis

We recommend the new guided biomass estimation tool which will take the operator
trough all details from survey planning to final report, optimize the system for each task
and give recommendations and background information. See the menu: Analysis=>Guided
analysis

To set up the system manually for biomass estimation, select Biomass from the
Analysis=>Analysis=>1-Setup menu or add an additional biomass window from the
Analysis =>Analysis=>Add. Menu. The first option will close all opened windows and
tune the system for Biomass analysis. The latter will add a Biomass window to the existing
setup. When at least one Biomass window is visible on the screen, the system is ready for
Biomass analysis.

Define a region to be analyzed and start the analysis. Simply drawing a rectangle with the
mouse in the echogram window can do this. Alternatively press the Analyze button in the
top panel of the Biomass window to specify region sub-regions, layers and start the
analysis. See chapter 4-Analyzing data for more information about setting up and starting
an analysis. The results will be presented in the different components in the opened
Biomass window(s).

Understand the use of the Amp and SED echogram

Amp and SED echograms are explained in chapter 6’s Amp and SED echogram section.
The sv/ts scaling method applied by the Biomass window integrates the energy from the
echo sounders amplitude detector seen in the Amp-echogram (total) and the energy from
the single echo detector seen in the SED-echogram (Trace). The estimations of the volume
and area of the sound beam defined for the Amp-echogram applies the concept of the
equivalent beam angle. The SED-beam is estimated from the transducers athwart and the
along ship opening angles defined by the beam compensation factor. Note that this is the
same as the -3dB angle only when the Max. gain comp. parameter was set to 3 in the single
echo detector. Other Max. gain comp values results in other opening angles. Thresholds are
also an important topic related to these echograms. See the Threshold section in this
chapter.

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The items in the Biomass window

The Biomass window contains the Region Grid, (RG) in the upper right corner, the Size
Group Chart (SGC) in the upper left corner, and the Size Group Grid (SGG) located at the
bottom of the Biomass window..

Region grid (RG)

The active cell in the RG is marked with a red rectangle in the echogram window and with
a stippled black rectangle in the Grid it self. The Biomass window’s Size Group Grid
(SGG) at the bottom of the window and the Size Group Chart (SGC) at the upper left part
of the window shows the results for the active cell.
Changing active cell is done by clicking the wanted cell with the mouse or by pressing the
keyboard’s arrow keys when the RG has focus. It has focus after each new region selection
in the echogram and whenever the grid is selected with the mouse.
The top row shows the pings that have been analyzed for each cell, while the left column
shows the ranges. The remaining cells displays a pair of numbers, the first number is
calculated from the amplitude echogram (Amp-echogram), while the second is calculated
from the single echo detection echogram (SED-echogram). The meaning of the presented
numbers is described in the panel above the RG. sA total and sA trace are presented by
default. However, other values can be selected in the Biomass 'window's control dialog.

Size Group Chart (SGC)

This chart shows the TS distributions of the single echoes located within the active sub-
region. In the Biomass control dialog, the operator can select the smallest size group, the
number of groups and the number of dB per group. See the section: Charts, in chapter 2 for
a general description of the chart.

Size Group Grid (SGG)

This grid, located at the bottom of the Biomass window, presents the total and the size
group results for the selected sub-region. In cases where there are too few single echo
detections, the cells will indicate low density. Low-density threshold is adjusted in the
control dialogs warning page (refer to low density threshold in this chapter).

The popup menu

Figure 86. The Biomass window's popup menu

Pressing the right mouse button in the Biomass window activates the Biomass popup
menu. The menu item is described below.

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Help
Selecting the help menu or pressing the F1 key when the Biomass window is active opens
this chapter.
Control dialog
Selecting the control dialog opens the Biomass window's control dialog. The control button
in the Biomass window's top panel can also open the dialog.
Layer segments and region selection
Selecting this menu item opens the echogram window's control dialog at the analysis page.
Here the region to be analyzed can be selected. Sub layers and sub segments can be
defined and the analysis started (See chapter 7).

Export

Figure 87. Export menu

Export extracts data from SonarX to other programs like Excel and Word. The "Include
menus defines whether a few or all the sonar parameters should be copied together with the
data.
Kubecka table
Export the content of the biomass basket formatted as seen in the basket. Selecting this
menu is the same as pressing the Export1 button in the biomass basket itself. Segments
(ESUs) are organized in successive columns and with parameters and results for each
segment in successive rows, After having presented all result for the first layer, next layer
are repeated at higher rows.
Winfield Table
This table organizes area, volume or biomass results for each sub layer in rows and with
results for each size group in columns. What to export is selected in the biomass control
dialogs export option page.
Monteoliva table
This option does also export the content of Kubecka biomass basket, but organized with
both segments and layers in rows and with parameters and results in columns. See also the
Result grid (What you see, but organized in rows) described below.
EP500-Table
This selection produces a table similar to the one that EP500 produced.

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All results
Select this menu item to produce a table containing everything that can be presented.
Sample values
Select this menu item to extract all the samples that have been analyzed. This menu was
implemented to test that the calculations actually were correct. The samples were pasted
into spreadsheets and the formulas, described in the end of this chapter, were applied to
recalculate what SonarX had calculated. Note that this menu option can be extensively
computer memory demanding id a large region covering many pings and meters have been
analyzed. The computer may run out of memory other programs running can then get
problems.
Result Grid (All)
This menu copies all the values that can be selected in the biomass control dialogs settings
page for all analysis cells seen in the result grid, including geographical positions.
Result grid (visible)
Copies what is on currently can see in the result grid.
Result grid (What you see but organized in rows)
Same organization as the Monteoliva table above but with the information presented in the
result grid and not taken from Kubeckas biomass basket.

Seg. Layer [From To [From To Total Sv SED GPS if

ping ping> R(m) R(m)> dB Sv dB available
1 1 306 406 8.3 9.8 -68 -70.5 -
1 2 306 406 9.8 11.4 -68.6 -69.6 -
1 3 306 406 11.4 12.9 -73.2 -75.8 -
Figure 88 Example of the Result grid (What you see but organized in rows) export option
Biomass basket

This submenu controls the biomass basket dialog. The dialog is a result collector.

Add will add the latest result to the basket dialog. First time something is added, the basket
will pop up in front of the other windows. It can be checked to stay on top but it will
otherwise work in the background.

View will bring the basket to the front of the screen if it is hidden behind other windows.
Note that the basket can be set up to stay on top and never hide behind other windows.

Close will close the basket.

Catch data scaling result
This menu opens the catch data scaling result dialog. The dialog scales the acoustic results
into different species and size groups according to catch data registered in the system
configuration dialog. Note that it is the result of the selected cell in the result grid that is
presented. Double clicking a cell in the result grid will open the Catch data scaling result
dialog for that cell.

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Sailed distance report will apply to the trace counting method. It is not implemented at
the moment.

Size group chart

Copies the size group chart. To alter the charts way of presenting the data, check the show
chart commander checkbox in the Biomass control dialog. Then use the different control
buttons appearing in the charts top panel to alter the view. Nearly all settings may be
changed. See Figure 89.

Figure 89. Size group chart with top panel for controlling the chart's appearance. The top-
panel appears upon checking the show chart commander checkbox in the Biomass control
dialog seen in Figure 91.

Biomass window
This export option exports a picture of the biomass window as seen when the export menu
is accessed.

Correct sonar parameters are important

To get correct results, the parameters involved in the calculations must be correct. The
parameters were originally set when the sonar file (*.dg *.raw) was converted. However,
neither the DG-file format nor the raw file format contains all the parameters needed by the
Biomass routines. Hence, erroneous settings might occur. Suspicious settings far out of
range will be checked automatically and warned against, but it can never be guaranteed
that all settings are correct. Pressing the parameter button in the Biomass control dialog
will open the basic parameter dialog. All parameters marked with green colors are
important for the calculation of Biomass. Enabled parameters were either obtained from
the original echogram file or they were directly involved in the conversion. Changing these
parameters at this stage in the analysis process will not improve anything. If believed to be
wrong one will have to redo the conversion or in the worst cases record the sonar files all
over with correct parameters.

Thresholds
It is important not to be confused by the different threshold definitions. There are the base
threshold, working thresholds, and warning thresholds.
Base threshold should be set so that it includes the background noise. The main trick is to
set the three working thresholds.

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Two Base thresholds

We recommend that the base thresholds are set below the background noise level which for
open water normally is somewhere between -100 and -120 dB. The two base thresholds are
set in the converter's initial parameter dialog accessed by the initial parameter buttons at
the converters first page. Base thresholds tell the converter about the lowest echo intensity
to be converted. Data below this threshold will not exist in the converted file and cannot be
seen or analyzed. A high base threshold will result in reduced file size, but may also result
in reduced performance of the analysis. We normally recommend including as much as
possible when applying the base threshold.

There is one base threshold for the Amp-echogram and another for the SED-echogram.
The base threshold for the SED echogram operates on off-axis compensated single echo
detections and is the same as Simrad's Min. value found in their single echo detectors.

Three Working thresholds

We recommend using the TS distribution dialog and for some situations also the Echmann
threshold window to find and set the appropriate thresholds. This and how to set the
thresholds is described in Chapter 4, section TS Distribution and Echmann threshold. The
TS distribution dialog can be opened with the biomass control dialogs Threshold button or
from the Analysis =>Data insight menu.

Technical description: No echo energy exists below the base thresholds. Thus, the base
threshold described above, defines a lowest boundary for all calculations. However, higher
working thresholds can be set to avoid noise or small fish. There are three working
thresholds. The working thresholds are the 1) Amp and 2) SED threshold located in the
Echogram control dialog's threshold page as described in chapter 7., and the 3) Start from
threshold located in the biomass control dialogs setting page. See the biomass control
dialog section in this chapter. See also setting of threshold with various TVG in chapter 6,
section TVG menu.

Amp working threshold

This threshold has the following properties.
 Can not be set below the AMP Base threshold
 Constant to the current echogram type (Sv or TSu) .
 Restrict what to be seen in the Amp-echogram
 Restrict what to be integrated. (Biomass, Macrophyte etc. )

SED working threshold

This threshold has the following properties.
 Can not be set below the SED Base threshold
 Always constant to TSc
 Restrict what to be seen in the SED-echogram
 Restrict what to be tracked by the tracker
 Restrict the Biomass size distribution when In situ SED or tracked SED are applied
as source.

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If set below the Size class Start from threshold in the biomass control dialog, the SED
working threshold will be automatically set to the same as the Start from threshold when
the first analysis is carried out.

The SED-working threshold influences on the generation of the biomass size distribution
while the Amp-working threshold influence on the echo integration. If set higher than the
Amp-base threshold, Amp-echogram samples below the threshold will be counted, but
they will not contribute to the integral with energy. (See M in Eq. 55.) Erased samples in
the Amp echogram and erased detections in the SED echogram will not be analyzed at all.
See the section; Erase unwanted echoes or noise in chapter 6

Start from threshold

Biomass estimation based on TS from single echo detection or tracked single echo
detections has a size distribution definition with a Start from, step and no groups. See the
biomass control dialog section in this chapter. The Start from is related to the SED
threshold and should normally be set equal to this.

When a region in the echogram is analyzed, and the biomass estimation method is based
on single echoes or tracked single echoes, only single echoes equal or larger than the Start
from threshold will contribute to the size distribution. The size distribution is then applied
to find the abundance for each size class step noted in the biomass size distribution
definition.

An easy way to set all the working thresholds

The TS distribution dialog is designed to help you setting the three working thresholds. It
let you study the size distribution and set the Start from threshold. This will automatically
set up both the size distribution in the biomass control dialog and the Amp and SED
thresholds in the echogram control dialog. The TS distribution dialog can be accessed with
the biomass control dialogs threshold button or by the main menu: Analysis=>data
insight=>TS distribution. See chapter 4, section TS distribution for more about how to set
the working thresholds.

Warning thresholds
The biomass control dialogs warning page has four different warnings activated by
individual on / off check boxes. When on, and if the given thresholds is exceeded, the
warning button in the biomass window will turn red. Clicking that button will open the
Biomass control dialogs warning page where all analysis cells that have raised a warning is
listed. Click a line in the warning list will present that cell in the echogram, in the biomass
windows result grid, and in the size distribution grid. Warnings are also reported in the
biomass basket and in exported tables based on the biomass basket.

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Figure 90 Biomass control dialogs warning page

Sawada index (Nv, M)

Two indexes, M where Nv are estimated and reported in the biomass basket, but currently
only the Nv is part of the warning system. Nv is the number of fish in the sampled volume
and M is the percent of multiple echoes Sawada et al (1993)
A common setting for the Nv warning is 0.1. (ref Great Lake standard operation procedure
ver 1.)

c
V  R 2
2

Nv  V   v

 v  ns
M  100
v

where:
V is the pulse volume at the mean range of the analyzed layer
c is the sound speed (m•s-1),
τ is the pulse duration (s),
ψ is the equivalent beam angle (ste-radians),
R is the mean range of the analyzed layer (m),
ρv is the volume density of targets (•m-3)
ns is the density of targets estimated from the single echoes

Number of SED
The #SED warning counts the number of SED in each analysis cell and warns if there are
fewer that set her. 20 to 50 SED is a descent number for biomass estimation based on the
sv / ts scaling method and in-situ SED as source.

sv sed / tot ratio %

The ratio between sv resolved as single echoes and the total sv in an analysis cell can
indicate whether the analysis results are reliable or not. Low ratio may be interpreted as too
much schooling with too few detection. The ratio is calculated according to the following
equation.

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sv SED
Eq. 50 ratio  100 ) : %
sv tot

svSED = linear volume reverberation calculated from echoes seen in the SED-echogram.
svtot =linear volume reverberation from the echoes seen in the amp-echogram.

TS max diff.
This warning compares TS of the largest and next largest single echo detection. It may be
that a big difference can indicate that echoes from bottom are included. 3dB may be a good
setting here.

Biomass control dialog

The Biomass control dialog can be activated from the Biomass window's popup menu and
from the control button on the Biomass windows top panel. The components in this dialog
are:

Apply button
Updates the Biomass window with the current settings without closing the dialog described
in chapter 10.
Close button
Closes the dialog
Analyse button
Start the analysis
Threshold button
Opens the Echogram control dialog on the threshold page. Analysis will not include echoes
below the current threshold setting in the Amp and the SED echogram.
Layers and segments Button
Opens the Echogram control dialog at the Analysis page. Here one controls the number of
sub segments and layers to divide a selected region into. See chapter 7.
Parameter button
Opens the sonar parameter dialog

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Figure 91. Biomass windows control dialog. Standard page

Result grid selector
This panel selects the estimate to be displayed in the Biomass window's result grid
Unit radio group
Defines the unit to be applied in the calculations.
Size groups panel
Defines the threshold, steps, and number of groups to be presented in the Biomass
window's size distribution. Selects also whether to present the results in dB, length or
weight. The two latter needs correct species and regression data to give correct results.
Misc. panel
No. of decimals
Controls the number of decimals.
Activate biomass window after each analysis
When checked the biomass window will be activated after each analysis. This ease the
analysis operation by that one immediately can use the keyboard arrow keys to switch
between the analysis cells presented in the biomass result grid and thereby easily run
through all results.

Water mud area density scaling

This setting influences the abundance and biomass area densities.
When checked on in the biomass control dialogs Settings page, (Figure 91) the abundance
and biomass area density for each analysis cell will be scaled according to the Water Mud
Ratio (WMR) obtained for each analysis cell. WMR is found by dividing the area covered
by water with the total area of the analysis cell. The Biomass basket will always report the

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WMR, but the Method description will indicate whether the scaling was applied to the area
density estimate or not. WMR is estimated according to the following equations:

WMR  AW / Atot

 bottomi  rupper 
P last
AW 
i  P first

 
Method 1: Atot  Plast  Pfirst  MaxBottom  rupper  w  h1 
 
Method 2: Atot  Plast  Pfirst  rlower  rupper  w  h2 
Figure 92 indicates the meaning of most of the involved variables. Aw is the Area covered
by water and Atot is the total area. Two methods for finding Atot are available. The selector
is located in the biomass control dialogs option page. Method 1 is the default method and
the one we normally recommend. rupper and rlower are the range where the analysis cell start
and stop, bottomi is the range where water changes to mud (or of course sand, gravel rock
etc.) for ping i. MaxBottom denotes the deepest part of the analysis cell. Pfirst and Plast
denotes the first and last ping in an analysis cell.

Method 1 is the default method if scaling is turned on. It will give the same scaling result
independent on whether one include much or little of the bottom when cell height is
selected. Hence the scaled surface area density will be the same independent of how deep
down into the mud a cell is stretching.

Method 2 can be selected in the menu: Utilities => System configuration => General
settings.
This WMR is comparable from cell to cell and reflects the topography of the bottom. For
thin analysis cells, this method can also be used to obtain reliable surface density scaling.

When to use the water mud ratio.

Assume a lake of 100 ha and that the analysis has been split up in two layers so that the
lower layer contain 50% bottom. Then assume that we find 10 fish / ha in both layers. If
we sum the area densities, we find a total surface area density of 20 fish / ha. If we
multiply with the surface area of 100ha we find that there must be 2000 fish in the lake.
This is, however, not correct since the lower layer only cover 50 ha. We must either
multiply the density in each layer with the actual size of the lake at the layer depth or scale
the area density in each layer before estimating the surface area density. When the Water
mud area density scaling is on, this is what is done.

The scaled area density for an analysis cell is then found by multiplying with the mean
WMR. In the example above, the analysis cell from the lower layer would have been
multiplied by 0.5. Summing would then result inn 10*0.5 + 10=15 fish / ha. If we now
multiply with the surface area of the lake we will find that the lake contains1500 fish and
not 2000 as erroneously estimated in the example. This is the same result as we would

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have found if we had multiplied the density at each layer with the actual lake area at the
layer depth and then summed up the results.
Cell width w (nr of pings)

Water
h1 h2
Mud

Figure 92 echogram analysis cell with water and mud.

Auto add results to biomass basket

When checked analysis results will automatically be added to the biomass basket after each
analysis.
Force presenting
These two checkboxes controls whether the amplitude echogram based and the SED based
estimates should be displayed in the biomass windows size distribution grid.
Show chart commander checkbox
If checked, a chart commander will appear above the chart in the Biomass window. The
commander controls most details in the way the chart is presented.

Figure 93. Biomass windows control dialog. Method page.

Species Id selector

Sonar5 has a species data base with regression equations for converting between TS length

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and weight. The main selector for this data base is located in the System configuration
dialog. This dialog can be opened by the Species ID button and for most operations we
recommend that Species are selected in the System configuration dialog. The biomass
control dialog has a local selector. Default is 0 witch means that the biomass analysis will
use the System configuration dialog’s selector. The local selector indicates this by telling
the selected specie. There are, however, a few situations where one want to force a biomass
window to use a regression different from what the rest of the system is set up to use. To
do so, changing the ID number in the local selector to an existing ID different from 0 will
do. (See also the Species page section in chapter)

Method radio group

Three different analysis methods can be selected.
Source radio group
Source can be single echo detections or tracked fish. When tracked fish are selected, fish
must be tracked and stored in a fish basket before the biomass analysis is performed.
Aspect correction radio group
De-convolution can be applied for horizontal mobile survey when the aspect is supposed to
be random and unknown. Track aspect can be applied when the aspect can be obtained
from the fish track as in fixed positioned horizontal surveys or when the transducer has
been mounted with a tilt in a vertical survey. NB! Both corrections needs selection of
species with correct regression information. (See Species button)
Survey type radio group
select between vertical and horizontal survey. Depending on Selected method additional
options will appear.
Transducer rotation radio group
indicates the rotation of a transducer when it is needed for the calculations. This depends
on the selected method and survey type and whether the transducer is circular or not.
Depth panel
The depth panel appears if the application is horizontal. Set the depth (thickness) of the
layer monitored by the transducer here. The value typed here is used to find the area
density of the investigated layer. This is done simply by dividing the reported volume
density with the typed layer depth.

Result output
Results are presented in the Biomass window itself, the Biomass basket dialog, the
Biomass and catch statistics dialog, and through the copy to clipboard function.

Biomass window output

The most important outputs from the biomass window are
1. sA,
2. Sv
3. Beam volume
4. Number of single echo detections or tracked fish
5. Fish per cubic meters

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6. Fish per m2, nm or ha

7. g, kg or ton per m2, nm or ha
8. Size distribution in dB, length or weight

Biomass basket
Like the fish baskets storing tracked targets, the biomass basket stores biomass. Each time
a set of layers and segments have been analyzed, the operator can press the A-key to add
the result to the basket. (Biomass window must be active) The basket stores the results
from each layer on separate spreadsheet pages and takes as many segments as the operator
has defined.
Presented data in the Biomass basket
Layer number The number of each analyzed layer indicated by the left
side tabulated pages.
Segment No: Caption numerating each stored segment result
Information Filename, species for regression, size distribution limits
etc.
Application Details about the application
Method Selected estimation method
Size distribution source Where the size distribution comes from
Segment start time: The time for the first analyzed ping in a segment
Amp-Threshold Threshold applied in the Amp echogram
SED-Echogram Threshold applied in the SED echogram
From ping First analyzed ping
To ping The ping after the last analyzed ping
# of pings Number of analyzed ping
Water mud ratio Ratio between the sum of beam height above and below
bottom in an analysis cell.
Min. range The layers start range. If a bottom layer is analyzed the
upper range will change with a changing bottom. Hence
the mean is calculated.
Max. range The layers end range. Mean is calculated if the range
changes with bottom throughout a segment.
Average range Mean lower + (Mean upper - MeanLower)/2
Average bottom depth or This is the average distance to the Max range line. For
Average max range This line is the bottom line in down looking applications
and the max range in horizontal and up-looking
applications
Volume of Amp-beam Based on equivalent beam angle.
Volume of SED-beam Based on the single echo detectors max gain
compensation parameter.
Surface area of Amp The projection of the Amp-beam upon the surface at the
beam average range
Surface area of SED The projection of the SED beam upon the surface at the
beam average range
Position start N/S Ship position if NMEA has been recorded
Position centre N/S Ship position if NMEA has been recorded
Position end N/S Ship position if NMEA has been recorded

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Position start E/W Ship position if NMEA has been recorded

Position centre E/W Ship position if NMEA has been recorded
Position end E/W Ship position if NMEA has been recorded
Sailed dist (m) Ship sailed distance in the segment
speed (m/s) Ship average speed in the segment
Volume Density* Total number of targets per 1000m3
Area density* Number of targets per surface area in units of g, kg or ton
Biomass* Biomass is estimated by means of the species selected in
the system configuration dialog. It is presented as weight
per surface area where the units are selected in the
biomass control dialog.
Average weight (gram) Average weighs of the targets.
Not used
Sv* (dB) Mean volume back scattering strength in the segment.
sA* Recalculations of Sv into area scattering coefficient in
selected area units. (m2, nm, ha)
Sv sed / tot ratio (%) Percent of volume reverberation represented by detected
single targets. Sv sed / tot ratio % See detailed
description in the section sv sed / tot ratio % in this
chapter.

Sawada index Nv See the section “Sawada index (Nv, M)” in this chapter
Sawada index Mv See the section “Sawada index (Nv, M)” in this chapter
Mean TSc (dB) Mean value of off axis compensated TS (dB) from the
single echo detections or tracked targets in an analysis
cell.
Warnings Report warnings set in the Biomass control dialogs
Warning page.
Detected single targets Number of tracked targets or single echo detections
Size distribution The remaining rows contain the number of targets in each
defined size group defined as TS, length or weight.
-50 dB Number of targets in the interval [-50... -47> dB
-47 dB Number of targets in the interval [-47... -44> dB
…… More size classes follows
* in the first column indicates that results for both total and trace are presented.

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Figure 94. Upper part of the Biomass basket. Results from each layer is found in separate
pages selected from the left side tabs marked 0 ..4.

Operating the biomass basket

The basket is operated from the biomass windows popup menu accessed by right mouse
click in the biomass window. Here menu “biomass basket” opens a sub menu with four
items;- New, Add, View, and Close. They have shortcuts such as N for New A for Add and
V for view. For smooth operation we recommend that one let the biomass basket stay in
the background, behind the echogram and biomass window, and press the A-key each time
one want to store a result. The basket will pop up in front of the other windows to show the
result, but will hide as soon as another window is activated with the mouse. Checking the
baskets Stay on top checkbox will prevent the hiding.
Biomass windows' popup menu

Figure 95. Biomass basket popup menu with short keys

Add (A): Add the last analyzed results to the active basket. If no basket is active, a new
basket is activated. Only new baskets will be brought into view. Existing baskets may be
hidden behind other windows. An accept-sound indicates that data has been added.

View (V): Bring the active basket into focus. If no basket is active, a new basket is
activated.

Close: Close the active basket. If this basket has been modified, the system will ask for
saving.

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The items in the Biomass basket

More functions are available directly from the basket than from the biomass windows
popup menu. The cells in the basket can be edited directly.

Add button. Adds the last analyzed result

Overwrite button overwrite the segments with the last analyzed results. Overwriting starts
at the segment indicated by the operator in the spin edit located above the button. The
number of defined segments in the echogram control dialog influence on the number of
segments to be overwritten.

Insert button: Inserts the last analyzed results after the segment indicated by the operator
in the spin edit located above the button.

Delete Button: Deletes the number of segments indicated in the echogram control dialogs
analyze page. Deleting starts at the segment indicated by the operator in the spin edit
located above the button.

Save and Load buttons: Save or load the contents of the basket to a binary file

Copy to clipboard button: Copies the contents of the basket to clipboard for transfer to
other programs

Stay on top check box: When checked the basket will stay on top and not hide behind
other windows.

Sound notification: When checked a sound will indicate when the content in the basket is
modified.

Important note: The label column is generated first time the basket is activated. Changing
settings in the biomass control dialog such as units will be reflected in the results added
after the change, but not in the labels or in the results added prior to the change. Sonar5
will indicate what to do if one tempts to change settings.

Ensuring the same layers to be analyzed for all segments

It may be difficult to ensure constant range for all analyzed segments when regions are
selected by drawing rectangles with the mouse in the echogram window. To assist in
getting the same layers analyzed for all segments, start the analysis by defining a pelagic
layer in the echogram control dialog's layer bottom and noise page. Focus on the layer if
necessary by setting the range in the manually in the echogram control dialog's vertical
page. Select numbers of sub layers in the echogram control dialogs analyze page. The
analysis will now be restricted to the defined layers except if the echogram is in zoomed
mode.

Alternatively, layers to be analyzed can be fixed from the echogram control dialog's
analyze page by noting the layers and using the analyze button to start the analysis.

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Export
The export menu contains various export options. The system will ask whether the selected
export format should be copied to clipboard or saved to file. See Figure 87.

Scaling the acoustic results to different fish species

Figure 96. Biomass window's scaled by catch data result dialog

Double click a cell in the biomass window's result grid will open this dialog. The
dialog presents the results for that cell scaled according to catch data. Enter catch data in
the system configuration dialog's "Catch data" page. Select the Utility system
configuration menu or press the button with the two fishes to enter the catch data editor.

Biomass estimation based on tracked fish

Both Single echo detections (SED) and tracked fish can be applied in biomass estimation.
If tracked fish is selected in the Source radio group, in the biomass control dialog, the

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biomass analysis will open selected fish baskets and look for tracked fish.

NB!
Our advice is to first focus on the tracking and storing of tracks, then turning of the
tracking and focus on the biomass estimation. However, tracking and biomass estimation
can be applied in the same operation.

Figure 97. Analysis=>Analysis=>1 setup menu. Alternatively use the newer

Analysis=>Setup menu
How to do it
1. Select “Advanced in the analysis menu as seen in Figure 97.
2. Select Track and biomass estimate at the same time in the appearing selector
3. Draw a rectangle with the mouse in the echogram window.

The program will track fish within the rectangle and store the tracks in a fish basket. Then
the stored tracks will be applied in the biomass estimation window.
Selecting source
It is the source panel in the biomass control dialog that determines whether tracked fish or
single echo detections shall be applied in the analysis.
Comparing results between SED and tracked fish input
Opening two different Biomass windows from the Analysis=>Data insight menu, tuning
one into using SED as a source and the other to apply tracked fish gives a simple way to
compare the two methods. The control dialog opened from one biomass window will only
control that window. This enables the use of multiple biomass windows with different
tuning

Multiple fish baskets

Fish can be stored in different fish basket. Only fish in selected baskets are applied. See the
classification window in the manual about selection of baskets.

Horizontal surveying
Area density expresses the fish density per unit surface area. For the biomass estimation
method based on sv/ts scaling, area density is obtained by multiplying the volume density
with the investigated water depth. This is simple for vertical applications. With horizontal

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surveying it is different. The volume density calculation is the same, but the transducers
tilt, opening angle and orientation (in case of an elliptical transducer) influences on the
investigated depth or the height of the beam. The section "Height of the beam" in this
chapter describes how Sonar5 calculates the height of a horizontally aligned beam.

The Biomass control dialog controls let the operator select various options for a
horizontally aligned transducer.

1. Open the Biomass control dialog and select Horizontal in the Survey type selector
2. Select transducer rotation and depth in the appearing selectors
3. Press the Parameter button, select advanced parameters and check that the transducer
tilt is correct.
4. Select the region to be analyzed in the echogram or echogram control dialog

For the biomass estimation method based on sv/ts scaling, the Area density will be
calculated as showed in the Eq. 51. For the echo counting and trace counting method the
volume and the proportion of the beam mapping to the surface are calculated.

 f / m    f / m  ( R  R )
2 3
2 1 Vertical
Eq. 51
 f / m    f / m  height
2 3
Horizontal

where height is the vertical part of the horizontally aligned beam. See the section "Height
of the beam" in this chapter.

Fish length and weight estimation

How to do it
Open the biomass control dialog and
1. Select the wanted aspect correction in the biomass control dialog.
2. Press the species button and select the species for the TS/Length /Weight conversion in
the appearing dialog (system configuration dialog).
3. Select size groups and units for the presentation in the biomass control dialog. (Length
in mm, cm and m and weight in g, kg or ton)
4. Select the region to be analyzed in the echogram or in the echogram control dialog.

Single species
Conversion between TS, length and weight is based on the regression equations located in
the species database. This database is described in chapter 11 System parameters in the
section “Species database page”.
The method for finding length and weight is this. The biomass control dialog has been set
up with a number of size classes. For example;- Start from=-70dB, step=3dB and
No.groups = 25. The average TS in each dB class are calculated in the linear domain. The
average TS in each class are converted to average length and average length is converted to
average weight with the TS/L and L/W regression equations related to the selected species
ID. With the average weight available for each size class, the biomass is found simply by
multiplying average weight with the abundance found for the same size class.

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Multi species
It is possible to select multiple species in the system configuration dialogs species selector.
Each selected species is then paired with a percent or probability of hitting that species
obtained from other sources such as catch data. The calculations of average weight are
done in the same way as for single species, except that the conversion now is based on the
average weighted by the probabilities.

  p Lreg (TS )
1
L i i center
N i 11

Where pi is the probablility for the i’th species, Lregi(TScenter) the length estimated by the

TS/Length regression inverted to output length. The procedure for finding the weight is

similar.

Aspect correction
Aspect correction is controlled by the Aspect correction panel located in the Biomass
windows control dialog’s method page. Available options are Off, De-convolution (hor.
mob.) and Track aspect with off as default.

Track aspect (fixed transducer)

This option does only apply when one of the fish basket options are selected in the size
distribution source panel, and should only be used to correct targets passing a fixed
transducer. Regression parameters from the species database are applied to calculate "true"
TS from the observed TS. The aspects for individual track, stored in the selected baskets,
are found by linear regression through the tracks individual echo positions.
De-convolution (horizontal mobile survey)
This option applies to mobile horizontal surveys and can be used when SED or fish baskets
are selected in the size distribution source panel. In a mobile horizontal survey, fish aspect
can not be obtained from the tracks. One solution then is to assume random orientation and
apply a de-convolution algorithm similar to Craig Forbes. The largest size class contains
echoes from the largest fish's seen from the side aspect. The second largest size class
contains the second largest fish plus the largest fish with some aspect, and so on. (Duncan
and Kubecka, 1995). Dr. Kubecka assisted in implementing the method in Sonar5.

Checking on the “De-convolution (hor. mob.)” will move the size distribution towards the
higher end, resulting in an increase in Mean TS and weight. Other estimates such as
volume and area density will not be influenced. The settings in the Size group selector
located in the biomass control dialogs “Settings page” is taken into account before the de-
convolution is carried out. If the unit is set to dB, then the de-convolution will be carried
out on size bins measured in dB and with the size classes indicated by the Start from and

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Step selectors. If the unit is set to Length, then the de-convolution will be carried out on
size bins measured in length and so on.

Figure 98 illustrates the implemented de-convolution method. Species selected in the

system configuration dialog provides the regression coefficients for the side and tail aspect.
The TS of the largest observed size group represent the largest fishes seen from the side.
This TS is converted to length and then to tail aspect to find the number of size groups that
may contain the largest fish seen from various aspects.

TS
TS versus fish length

Side aspect

Tail aspect

Observed size
distribution length
Figure 98. Illustrating de-convolution of observed size distribution.

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SED-Echogram

Tracked
fish
TSc
TSu MeanTSc

Observed
Size Dist

Aspect correction De-convolution

Interpreted
Size Dist

TSu   svu SED

N , n k , ts k

f / m3   1
svu
N

N
n k ts k
k 1

Figure 99. Aspect correction with tracked fish or single targets as input. Switches in the
biomass control dialog controls the signal flow. k indicate the size group.

Trouble shooting
Why do I only see 0's in the result grid and no histogram in the size group chart?
The size group parameter "Start from" in the Biomass control dialog has been set to a value
greater than the echo intensities found in the echogram. Change the "Start from" value and
press update in the control dialog will do.

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Calculations
If a region is defined in the echogram window when a Biomass window has been opened,
the region will be analyzed by the Biomass window. A region is defined as [P1...P2> and
[R1... R2> where P and R are ping and range respectively. The region is divided into a
number of sub-regions and sub-segments depending on the values set in the echogram
control dialog's analyze page. (See chapter 7).

The fundamental calculations of target range TS, and Sv is described in Chapter5, section
sonar equations

Calculating mean sv and sA

The SED-echogram consist of a number of single echo detections believed to origin from
single targets. Each detection is represented with a point in time and space and with
defined target strength. We find the average TS in the linear domain (  bs ) by the
following formula

1 N TSc ,i

Eq. 52  bs  10 10
N i 1
where N is the number of detections and TSc, i is the off-axis compensated target strength
of the ith detection.

The Amp-echogram consists of Sv or TSu sample values where u indicates that the values
are not off-axis compensated. Each sample may represent e.g. 3 cm of the water column
from one ping. The sample values represent both schools and single fish traces. If we
integrate everything, both schools and single fish traces, we find the mean Sv_total. If we
integrate Sv samples only origin from single fish traces, we find the mean Sv_SED.
Technically, Sonar5 uses the single echo detections in the SED echogram and redetect all
the samples that originally caused the detection. Depending on the echo sounder system,
one single echo from a single fish trace may contain from 3 to 24 samples in the Amp
echogram.

SonarX uses the range of the detected single echoes as an indication on where to find the
original trace in the Amp-echogram. A detection algorithm re-detects the original samples.
If the Amp echogram samples represent TSu values, each sample are converted into Sv
values. The re-detected samples are summed in the linear domain and divided by the total
number of involved samples (M) within the analyzed region, in order to find the mean
Svu_SED.

Sv amp (i , j )
Stop _ i
1 N
Sv SED    10
M i 1 j  Start _ i
10

Eq. 53
sASED  SvuSED  R2  R1   4  AreaUnit

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Were M is the total number of involved samples in an analysis cell as described in Eq. 54.
N is the number of single echo detections from all traces in the analysis cell. The index j
run over all samples forming the shape of each individual single echo. R2 and R1 is the
upper and lower analysis cell boundary.

The total number of samples, involved in an analysis, is calculated with one of the
following formula.

P2
 R2i  R1i 
Eq. 54 M   R
 Erased i 

( * see comment )
i  P1

where i running from P1 to P2, denotes the ith ping, R the range resolution measured in
meters per sample, R2i-R1i is the analyzed range for each individual ping. R2i, R1i may vary
from ping to ping in cases of interference from bottom or analysis of bottom layers. Erasedi
is the number of samples within the selected region that have been erased by the operator
as noise. (See the section Erase unwanted echoes in chapter 6.) Samples below the
threshold are counted, but they do not contribute to the echo integration. Samples erased by
the operator are excluded as non-existing samples.

* Comment: For Sonar5, the equation for M can be altered. The selector is located in the
System configuration dialogs General Page. See section Controlling the divisor for
averaging in chapter 11.

Sv_Amp and sA _Amp (Mean volume backscattering strength, and mean area scattering
coefficient) are calculated by summing all the Sv values found in the amp echogram.

P2 R2 ,i Svi , j
1
sv 
M
 10 10
i  P1 j  R1,i
Eq. 55
P2 R2 ,i Svi , j

 R2i  R1i   4  AreaUnit

1
sA 
M
 10 10

i  P1 j  R1,i

M = Number of samples in the Amp-echogram as described above and P= ping. R2, R1 may
vary from ping to ping. Hence, (R2-R1) has to be found for each ping to calculate the
correct sA. If the Amp-echogram has been interpreted with the point sonar equation,
normally associated with the 40logR TVG, the echo intensity is converted to volume
reverberation (Sv)

Area density
Area density the volume density projected on to the surface so that one later can find the
number of fish in a lake by multiplying with the total area of the lake. The lake bathymetry

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must be included in the calculations either by scaling the density from various layers with
the water mud ratio (wmr) or by multiplying with the appropriate area at the depth in
question.

Area density for vertical applications

For analysis cells, not influenced by bottom, area density can be found by multiplying the
volume density with the thickness of the layer. When a cell is influenced by bottom, each
ping must be analyzed independently, because of the ping to ping variation in the actual
layer thickness.

Svi , j
P2 R2,i
1
  10 10 R2,i  R1,i 
M i  P1 j  R1,i
AreaDens  TSci
1 N
10
N i 1
10

Where M is the number of samples in the analysis cell above bottom, N the number of
single echo detections, P is ping number, R1 is the layer start and R2 the layer stop or the
bottom. The nominator gives the sA while the denominator gives the mean linear TS or σBS

Not that we cannot find the area density under influence of bottom by multiplying the
volume density with the mean layer thickness.

 R2,i  R1,i 
1 P2
MeanThickness 
P i  P1

AreaDens  VolDens  MeanThickness

Where P is number of analyzed pings.

The four biomass estimation methods

The echo sounder measure the power received by the transducer. Integrating this power
over time gives the energy. This energy can be interpreted as the returned backscattering
coefficient from a unit volume

sv=Σσbs/V, [m-1]

or a unit area
R
sa   sv dR , [m m ].
1 2 -2
R2

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For historical reasons, the scaled area scattering coefficient sA are commonly used as the
area coefficient (as in Sonar5). sA relates to sa by the chosen area unit (e.g. A=18522 when
working with square nautical miles, or A=104 when working with hectares) and a factor of
4π, such that sA=sa4πA. If mentioned in their logarithmic domain, the letter s in these
symbols is capitalized. For scattering targets, the back-scattering cross-section (σbs, [m2])
also relates to spherical scattering cross-section (σsp, [m2]) by a factor of 4π (see Eq. 10).

Knowing the target strength from each individual fish in this volume or area enable us to
estimate the fish density. To find the target strength distribution, one can apply catch data
together with empirical knowledge of the TS versus fish length relationship, or one can
apply in-situ target strength measurements. The latter involves single echo detection or
single echo detection and tracking. Tracking reduces the variability in the distribution.

The fish density can be found in many ways

 Sv / TS scaling
 Echo counting
 Trace counting
 Single beam (Craig & Forbes deconvolution)

sv/ts scaling is implemented in both Sonar4 and Sonar5-Pro while the remaining methods
are available in Sonar5-Pro only. In Sonar4 the method relates to vertical applications
while Sonar5 can apply the methods to both vertical and horizontal applications. In
horizontal applications the height of the beam (investigated depth) can be user defined or
calculated automatically. If an elliptical beam has been applied the operator can select its
rotation. For the sv/ts scaling method both tracked fish and single echo detections can be
applied.

When catch data are applied, each fish in the catch basked are converted to a traditional
track in the fish basket. All methods calculate the total fish abundance by multiplying the
single target result by the ratio between total and single target volume back scatter.

Biomass estimation based on sv /ts scaling

The sv/ts scaling method uses Sv and TS in their linear domain, i.e. sv and σbs, respectively.
Fish density
The Volume density ρv defines the number of fish per unit volume of water. E.g. #fish/m3
The fish density can also be expressed as the number of fish per unit area of the surface.
These fish are found in the water column below a unit area of the sea surface.
Ru
Eq. 56 a   v dR
Rl

If the volume density is constant over the layer in question this can be expressed as

Eq. 57  a  v ( Rl  Ru )

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In the case where all fish have equal and known back scattering coefficient (σbs), and
where we observe the unit volume back scattering coefficient (sv = Σσbs) we can write

Eq. 58 sv  v   bs

if we have 5 fish with σbs1 and 3 fish with σbs 2 the contribution to sv from the two
sizeclasses will be
5 n
sv1  1   bs1  v bs1  i v bs1
8 N
Eq. 59 3 n
sv 2   2   bs 2  v bs 2  2 v bs 2
8 N
Summing the two equations gives

ni n
sv1  sv 2      bs1  2     bs 2
N N
  N

Eq. 60 sv 
N
 n1 bs1  n2 bs 2  
N
n 
k i
k bs k

sv
 N
1
N
n 
k i
k bs k

N is the total number of detections, k indicates the kth size class and
nk the number of detections in size class k. The size classes are obtained from the linear
off-axis compensated target strength (TSc) single echo detections values.

This equation is implemented in SonarX to find the

N
1
 bs k 
N
n 
k i
k bs k

Eq. 61  f / m   s
3 v
):fish per unit vol.
bs k

 
 f / m    s
2 A
 ):fish per unit area
 bs k 

Where  bs k is the average off-axis compensated backscattering cross-section of the kth size
class. svused and sAsed is defined in Eq. 52 and Eq. 53.

We can also find the individual densities by scaling the total fish density by the ratios nk/N.

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Eq. 62 f /m 2
SED k 
nj
N
f /m  2
SED

The total fish density is found by replacing svused and sAsed with svuamp and sAamp in the
above equations.

Applying tracked fish

When tracked fish are applied, sv and ts is calculated from the individual single echo
detections in all the applied tracks while N are the number of tracks and nk the number of
tracks in size group k, not the number of detections.

Total abundacne

f / m   f / m
2
Total k
2
sin gle k 
sv Amp
sv SED
Eq. 63

f / m   f / m
3
Total k
3
sin gle k 
sv Amp
sv SED
sv is defined in Eq. 55. Amp indicates the amp echogram containting the total volume back
scatter while SED denotes the single echo detections. k indicates the kth size group. Even
when tracked fish are applied the track's single echo detections are used for this
calculation.

Biomass estimation based echo counting

Single echo detections as source

# echoes   f / m3    f / msin gle k 

3 sv Amp
sv SED

With the echo counting method, area density (f/m2) is found by calculating the mean
number of single echo detections per ping, dividing by the volume of the beam and
multiplying with the height of the beam.

f / m 3
Single k 
# SED n 
 k 
# Ping  Vol  N 
Eq. 64
f / m 2
Single k 
# SED n 
 k 
# Ping  Area  N 

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Tracked fish as source

Tracked fish can be applied in similar way as in the Sv/ TS based method. The number of
detections #SED is found from the sum of single echo detections within the tracks while nk
and N are found from the size distribution generated from mean TS of the tracked fish.
Volume is the volume of the beam defined by the single echo detectors Max gain comp
parameter and the -3dB opening angle.

f /m 3

Single k 
nk # SED
N # Ping  Vol
Eq. 65
f /m 2

Single k
n
 k
# SED
N # Ping  Area

The above equation gives the number of targets per volume or area that have been resolved
as single echo detections. To find the total, this is multiplied with the ratio between the
mean volume back scattering area of the total and the single echo detections.

Biomass estimation based on the trace counting method

This method applies only to situations where fish has been tracked and stored in a fish
basket. When this method is selected in the biomass control dialog, the source selector will
be locked to tracked fish. The operator can still select vertical or horizontal survey and
weather the transducer was mounted with athwart ship axis in the ship's sailing direction or
in the ships athwart direction.

Volume and Area:

Sonar5 stores navigation information in a separate file distinguished from the echogram
file name by the extension *.nav. This file contains registrations of the boat position along
each transect. There are normally a few pings between each position registration. Sonar5
determines the distance sailed between two and two ship positions and divides this by the
number of pings transmitted between the two registrations. This gives the average sailed
distance between subsequent pings. Volume (vw) and surface area (aw) are calculated from
the wedge formed by the sailed distance per ping, the range and the Wedge Opening Angle
(WOA), and the range. If bottom or bottom layer is presented in the echogram, these will
be taken into account. The WOA is calculated from the single echo detection criterion
“Max gain Comp”. If “Max Gain Comp” is set to 3dB (one way) then WOA will be equal
to the transducers opening angle in the athwart ship domain. For elliptical transducers it is
important to tell the system how the transducer was mounted. This is done in the menu:
Utilities=> Parameters=>Application.

Output in the Biomass window and basket:

For Trace counting, use the numbers suffixed with tracks. E.g. “Volume Density
(#/1000m^3) tracks” This contain the results from the trace counting method where
number of tracks in the fish basket has been divided by the estimated sailed volume or
covered area. The Biomass window and the Biomass basket do also output another number
suffixed “total”. E.g. “Volume Density (#/1000m^3) total (scaled from tracks)”. Total
means that the estimate involve the amplitude echogram containing the total echo energy,
and not only single echo detections in a track. For sv/ts scaling, values suffixed with

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“total” is the basic figure to use while the figures suffixed with “trace” only serves as
control figures. For trace counting, however, this is opposite since the densities based on
tracks are the main and important estimate. For trace counting, the total is simply a scaling
telling something about the ratio between the energies in the two echograms.

When the area and volume has been estimated the entire abundance for the analyzed part
of the transect and layer is found according to the following equation

Eq. 66 f /m  3
tracks

# tracks
vw

Where # tracks = number of tracks found in the selected fish basket for the actual part of
the survey covered by the estimated wedge volume vw. vw = observed volume for the
sailed distance, layer in question and WOA as described above. Area density is found in
the same way by exchanging the volume for the estimated wedge area (aw).

To find the abundance for each size class the entire abundance estimated above is scaled
by the ratio between the numbers of tracks in each size class (k) to the entire estimate N

Eq. 67 f /m  3
  f / m 3 tracks   k 
n 
tracks, k
N
Where N = entire number of tracks and nk = number of tracks in size class k

Although not important and mainly not useful, the system does also scale the abundance
estimates with the ratios between the total energy in the amp echogram and the energy
represented by the tracks to output the figures with suffix total such as “Volume density
(#/1000m^3) total (scaled from tracks)”

Warning
While the sv/ts scaling and the echo counting method work with the observed echoes in the
beam formed by individual pings, trace counting works with observed targets relative to an
estimated wedge formed beam. If the speed of the boat increases too much relative to the
ping rate this wedge start to deform. Deformation influences both on the estimated volume
vw and area aw and on the formation of tracks during the tracking process. Hence, the
effect on the resulting abundance estimate may be difficult to predict. The Mouse Tip
Monitor found in the echogram menu can show and log the degree of beam overlap
everywhere in the echogram.

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Figure 100. Crossection of true sampling area with non overlapping beams (upper), with
semi overlapping beams (centre) and overestimated area calculated from the beam-width
and the saild distance (lower).

Biomass estimation based on tracks and catch data.

While the other methods compare single echo detections or tracks found within the
analyzed region in the echogram, this method simply applies tracks from everywhere.
Hence the tracks may come from tracked fish in the file, from other files or from catch
data. Tracks can be generated from catch data as described in the sections catch data and
species database in chapter 11. The tracks are applied to establish the size distribution, to
scale the total echo integral (Sv-Amp), and to obtain the total abundance.

Vertical versus horizontal beaming

The meaning of the calculated values depends on whether the beam is directed down wards
or sideways.

Finding the mean range Rm that divides the beam in two equal parts.
Mean range is needed to find the height of the beam and to find the surface area. This
range is the range that divides the sound beam into two equal volumes. Hence solving the
following equation gives Rm.

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V1  V2
Rm R2
 A( R)  dR   A( R)  dR
R1 Rm

Eq. 68 
3
'  ' 
2
  
3
'
2

 ' 
 tan    tan   Rm3  R13   tan    tan   R23  Rm3
2 2

Rm3  R13  R23  Rm3
2 Rm3  R13  R23
R13  R23
Rm  3
2

where V=Volume, R=Range, ' and ' the Max gain compensated opening angle of the
SED beam.

Beam height, volume and area

Height of the beam
The height of the beam is important in order to calculate sA since

s A  sv  height  4

sA is also applied in the echo counting method based on sA/ts scailing.

Height (h) of a vertically alligned beam

In the vertical case, observed height is simply R2-R1.

R1

R2

Figure 101. Height of the vertical sound beam. (h=R2-R1)

Height (h) of a horizontally aligned beam

The height of a horizontally aligned sound beam is found at the range Rm that divides the
applied part of the sound beam in two equal volumes. Rm is developed in Eq. 68.

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 
Eq. 69 h  2  Rm  tan  
2

h

Rm

R1 R2

Figure 102 . Height h along the vertical axis of a horizontally alligned sound beam.

h in Figure 102 is, however, only valid for a rectangular beam. If we take into account that
the beam shape is circular or elliptic, the average height is less than the height found along
the centre line.

If we look at the height h0..h4 in Figure 103, it is clear that the mean height of the upper
right quadrant will be the sum of the individual heights h0..h4 divided by the number of
measured heights.

If we look at the height h0..h4 in Figure 103, it is clear that the mean height will be the sum
of the individual heights h0..h4 divided by the number of measured heights.
b

0 h0 h1 h2 h3 h4 a

Figure 103. The heights of a horisontally alligned beam depend on where on the axis it is
measured. a and b is the main and semiaxis of the ellipse.

We can find the mean height by integrating the heights along the horizontal axis. For an
ellipse, the height h at any point along the horizontal axis x is

b 2
Eq. 70 h2 a  x2
a
hence, the mean height of the quadrant is

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ba 2

a0
a  x 2 dx
Eq. 71 h  2
a
 dx
0
solving the nominator gives

a
ba 2 b x 2 a2 1  x  
       
2 2

a  a 
a x dx a x sin C
a0 2 a 0
Eq. 72
b a2 a2   a b
  sin 1  sin 1 0 
1

a 2 2  4

while the denominator simply results in the main axis “a” witch is the distance form origo
to the rim along the main axis. Division gives the mean height

 a b
4  b
Eq. 73 h  2 
a 2

, which is the mean height of the right side of the ellipse. By symmetry this will be the
same as the mean height of the left side of the ellipse.

From the transducers horizontal and vertical opening angle , , and the distance R from
the transducer, a and b can be found as

 
Eq. 74 a  Rm tan ,
 
b  Rm tan 
2 2
If the beam is tilted some degrees from the horizontal, the vertical axis will increase. If  is
the vertical opening angle, the semi axis b will be elongated to b' as seen from Figure 104. .

Rm tan  
b 
b
  2
costilt  costilt 
Eq. 75

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
 b'

b h

R1
Rm
R2

Figure 104 . Investigated depth by a tilted sound beam.  is the here the vertical opening
angle.  is the tilt and h is the height of the beam at range R. Equation Eq. 76 is valid when
the single echo detectors max gain compensation (mgc) parameter is set -3dB. Increasing
or decreasing this parameter will influence on the effectiv opening angle. Hence, we must
include the mgc parameter as defined in Eq. 79.

  Rm tan   2 
  b  
Eq. 76 h  
2 2  costilt 

Figure 105 . Inserting the transducers alongship opening angle into Eq. 76 gives the height
of the left ellipse while inserting the atwarthship angle gives the height of the ellipse seen
to the right.

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Volume and area of the Amp and SED beam

ath/2
R1

V1 Area Rm

Rm r1
r2 a
b
V2
R2

Figure 106. Left: Area of the beam at the mean range (Rm) dividing the volume between R1
and R2 into two equal volumes. Right: Cross section of the beam down to Rm, illustrating
the components a and b applied to find the surface area.

The sonar system applies two different sound beam definitions. These are the sound beams
defined by
a) The Single Echo Detector resulting in the SED Echogram. (SED-Beam)
b) The Envelope Detector to producing the Amp-echogram. (AMP-Beam)

These two beams are controlled by different parameters and may differ in size.

Opening angle and the Max. gain comp. parameter

When the echo sounder detects single echoes (SED), no echoes will be accepted outside
the single echo detectors Max. Gain Comp. (MGC) criterion. Hence, MGC defines the
beam’s opening angle. When calculating the Sv contribution from the single echo
detections, we have to apply the actual beam applied by the single echo detector and not
the beam defined by the 3dB opening angles.

The actual opening angle x and y can be found from the following equation when MGC is
known.

       off
2 2
    off     off
2 2
Eq. 77 MGC  3  Off
  

  0.18     

 
   em / 2   em / 2    em / 2   em / 2  
 
Here ,  are respectively the along ship and athwart ship angle, off , off respectively the
along ship and athwart ship offset and em ,em the electric to mechanical conversion
factors.
  off 
2
Eq. 78 k1    , k 2  0.18k1
  em / 2 

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MGC
 k1
Eq. 79    off   em  3
1  k2 
With Alo= and Ath= we find the area and the volume of the SED-beam from the ellipse
equation.

Defining the AMP-Beam (total beam).

From the volume reverberation model it is seen that the volume in the σv is based on the
equivalent beam angle . All calculations regarding the area and volume of the Amp-beam
should therefore be calculated from equations involving the equivalent beam angle. If the
beam angle is not known, it can be modeled from the transducers -3 dB opening angles.

10 log( )  (20 log  / 2)  31.6 Circular transducer

Eq. 80
10log ( )  (10 log  a  b / 4)  31.6 Rectangular transducer
Here  denotes the full opening angle in degrees measured at the -3 dB points (one way).
From the second formula  can be extracted as:
31.6
 a  b  10 10
Eq. 81  Rectangular transducer
4

Area and volume of the Amp beam (total beam)

When  is known we can find the area of the Amp-beam at a defined range

dA  R 2 d
Eq. 82 
A   R 2 d  R 2
0

And the volume

R2
V  R dR
2

Eq. 83 R1

1
V   ( R23  R13 )
3
Where R is the range or distance from the transducer and  the equivalent beam angle. To
test the formula one can set =4, which gives the well-known volume of a sphere.

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Volume of the SED beam (trace beam).

The volume of the SED beam is found by integrating the elliptical beam cross section area
from R1 to R2 where R1 denotes the upper and R2 the lower range or depth.
R2

V   A( R)dR
R1

 2  tanath 2  dR
R2

Eq. 84 V     R 2 tan alo

R1

1
3
   
V    tan alo  tan ath  ( R23  R13 )
2 2

Where ' and ' are the opening angles calculated from the SED beams Max. Gain Comp.
parameter MGC. R is the range. Vi is the volume at the ith ping and mean V from all pings
in the investigated segment. a and b is the length of the main and semi-axis of the ellipse as
defined in Eq. 86

Surface area of a vertically aligned SED beam

The echo counting and trace counting methods uses this area in the calculation of the area
density.

This is the sound-beam's cross section area found at the depth Rm that divides the
investigated layer into two equal volumes. Rm is found in Eq. 68

Eq. 85 Aellipse    a  b

The area A is then found to be

 2
a  R  tan  
Eq. 86

b  R  tan   
 2
'   ' 
Eq. 87 A    a  b    Rm2  tan   tan 
2 2
where a and b is the main and semi-axis of the ellipse formed by the transducer and ' and
' are the transducer opening angles influenced by the Max gain compensation parameter
as described in Eq. 79..

Surface area of a horizontally aligned SED beam with tilt

While a vertically aligned beam project an elliptical shadow area on the surface, the
horizontal beam projects a triangle. With increasing tilt, the projected triangle will look
shorter with a wider opening angle. Due to the circular or elliptical shape, the opening
angle of the projection must be calculated from the average beam width. The beam and its

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surface projection are indicated in Figure 107. Due to the symmetry we can find the mean
beam-width at Rm and treat the beam as a rectangle to simplify calculations. Note that the
rotation of the beam is important with elliptical beams.

Aproj

R1

R2 w

Figure 107. Tilted beam with mean width and surface projected area.

The mean width (w) is found in the same way as the mean height in Eq. 76 except that we
use the horizontal angle and not the vertical. We also omit the cosine factor.

w( R) 
  R  tan  2  
Eq. 88 2

This is the 2-sided width of the beam at an arbitrary range (R) according Figure 107.  is
the horizontal opening angle and will for the SED beam depend on the single echo
detectors max gain comp. parameter.

When the area is projected on the surface, the range R will be shortened by a factor cosine
of the transducer tilt. The surface area of the projected beam is found by integrating w(R)
from R1 to R2

 2  R  costilt   tan  2 dR

R2 R2

A   wdR 
R1 R1
Eq. 89
A

4
 2  R
 tan  2
2  R12   costilt 

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Which is the surface area calculated by Sonar5 when a circular or elliptical sound beam is
aligned horizontally or tilted downwards from the surface.

When the operator selects to define the dept manually instead of letting the system
calculate the depth, the area will be the volume divided by the depth.

Volume covered by a moving transducer

The echo counting method based on trace counting needs this volume and area. The
volume is calculated from the wedge formed by the ship movement and the athwart-ship
opening-angle influenced by the max. gain comp. factor as defined in Eq. 79. The width
(w) is expressed as a function of range (R). Multiplying with the sailed distance gives the
area at an arbitrary range. Integration of this area across the layer gives the volume. To
allow bottom layers and variable bottom the calculation is performed between each
individual ping and summed up.

  
w( R)   R  tan  
2 2
R2
Vi   w( R )  d i ,i 1i dR
R1
R2
  
Eq. 90 Vi   2  R  tan 2   d i ,i1i dR
R1

  
Vi   tan    d i ,i 1 R22,i  R12,i 
2 2
P 1
Vol Sailed  Vi
i 1

Where w(R)i is the width of the beam at an arbitrary depth at ping i.  is the transducer
opening angle that points in the athwart direction and calculated according to the applied
single echo detector's Max Gain comp. factor. Vi the volume between ping i and i+1, di is
the sailed distance between ping i and i+1 R1,i and R2,i the upper and lower bounds of the
investigated layer.

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Pos 2
Pos 1 di

ath

R1 Ping 3

R w Ping 2
Ping 1
R2

Figure 108. Volume of a transect between two successive position registrations in a bottom
layer.

Surface area of a vertically aligned, moving transducer

The surface area is found as the area of the cross section at the depth that divides the
volume of the wedge in the investigated layers into two equal halve.
R12,i  R22,i
Rm ,i 
2
 
wm  2  Rm  tan  
Eq. 91 2
Ai  wm  d i ,i 1i
P 1
Area Sailed   Ai
i 1

Where wm is the width of the beam at the range Rm that divides the ith volume segment into
two equal volumes. di is the sailed distance between ping i and i+1 R1,i and R2,i the upper
and lower bounds of the investigated layer.  is the transducer opening angle that points in
the athwart direction and calculated according to the applied single echo detector's Max
Gain comp. factor. Ai is the area between ping i and i+1.

Surface area covered by a horizontally aligned, moving transducer

When the beam is horizontally aligned, the volume will be the same as in the vertical
application. However, the area will not. This is indicated in Figure 109. Here the area AP is
found from the projected range RP and the sailed distance d. The projected range is scaled
according to the tilt of the beam.

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R proj  R2  R1 cos(tilt )

Eq. 92
APr oj  R proj  d

where A=area , R the range and d the sailed distance as defined in Figure 109. The
subscript p denotes projected variables. In cases of varying range applied e.g to avoid
noise, Ap is summed up from the mean range observed between each navigation position.
Note that this calculation is not influenced by the rotation of the beam.

AP

d=sailed dist.
Rp disr

R1

R2 acoustic axis

Figure 109. Projection of the tilted beam to the surface.

Parameters involved in the Biomass calculations

As seen from the equations above the following parameters are important for the
calculations.
Symb. Parameter name Description Used for
 Absorption_coeff Absorption coefficient TS and Sv estimation.
icient (dB/km)
c Sound_Speed Sound speed in water Range and wavelength.
(m/s)
 Tr_Pulse_Length Transmitted pulse length Sv, Pulse volumen, TS and Sv
(ms) conversion.
P Tr_Power (W) Transmitted power TS, Sv
f Tr_Sound_Freq Transducer sound Wavelength
(kHz) frequency
GSv Tr_Sv_Gain (dB) Transducer Sv gain Sv, Conversion Sv ,TS
GTS Tr_TS_Gain Transducer TS gain TS, Conversion Sv,TS
(dB)

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 Tr_2- Transducer 2 way beam Sv, Volume and Area of the Amp
WayBeamAngle angle beam
(dB)
MBC Max. Gain Comp Single echo detection Volume and Area of the SED beam
criterion
3dB Tr_3dB_Beam_ Transducer -3dB along Calculate  if unknown
Width_Alo (deg) ship opening angle
3dB Tr_3dB_Beam_ Transducer -3dB athwart Calculate  if unknown
Width_Ath (deg) ship opening angle

Biomass estimation based on Sv / TS scaling, a

calculation example
Assume that we have 2 fish with TS=-40dB in the beam and that one is positioned at 10
meter and the second 12m from the transducer. We will now calculate the backscattering
coefficient, the average TS and then the abundance per cubic meter of water. The first we
must do is to calculate the pulse volume at the range of each fish.

19
c 2 1500m / s  0.3ms
v(10m)  R   10 2 m 2  10 10  0.206495m 3
2 2
v(12m)  0.297353m 3

Now Sv can be found from TS, remembering that σp≡σbs.

G TS2  bs
sv  
G Sv2 V

assuming that the two gains are equal we find

TS 40
10 10
10 10
s v (10m)    0.000484m 2 /m 3
v(10m) 0.206495
TS 40
10 10
10 10
s v (12m)    0.000336m 2 /m 3
v(12m) 0.297353

With sv=10Sv/10 and σbs=10TS/10 we have that the average sv = (0.000484 + 0.000336)/2
=0.00041 m2/m3 and the average σbs = 10-40/10=0.0001 m2

The density is

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s v     bs
sv 0.00041
   4.102886 fish/m 3
 bs 0.0001

The two fish was observer in a water volume of v(10m) +v(12m) = 0.503848 m3 and if we
multiply the calculated density with this we find the number of fish we started with.

As seen above we applied the investigated volume and not the volume of the beam within a
layer such as 10 to 12 meters If we apply this volume we will get too many fish. With the
applied equivalent beam opening angle of -19dB the this volume will be
R2
1 1
V   R 2dR   ( R23  R13 )  10 19/10 (123  103 )  9.6607m3
R1
3 3

and the number of fish will be

# fish  V  0.94m-3  9.66m3  9.1 fish

The number of fish will continue to increase if the layer increases without more fish being
observed. If the fish density is constant, we will find the same number of fish with any
layer thickness.

For this method to work correct, we must have sufficiently high fish density so that the
there are observations in all the pulse shells.

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Main menu

BOTTOM PROFILE AND TRANSDUCER POSITION ......................................................................................................228

Drawing a new bottom profile .........................................................................................................................229
Delete the bottom profile ..................................................................................................................................229
Predicting the optimal transducer position in a river or a lake .......................................................................229
Edit the bottom profile .....................................................................................................................................229
Exporting and importing bottom profiles .........................................................................................................229
Importing bottom profiles during conversion ..................................................................................................229
COPY TO CLIP BOARD.............................................................................................................................................230
DISPLAY MODES ....................................................................................................................................................230
HELP ......................................................................................................................................................................231
MAIN POP-UP MENU ...............................................................................................................................................231
MEASURING DISTANCES ........................................................................................................................................180
POSIGRAM CONTROL DIALOG.................................................................................................................................181
Main page ........................................................................................................................................................181
TRACK INFORMATION DIALOG ...............................................................................................................................182
The numerical track presentation page ............................................................................................................182
Description of the presented echo attributes ....................................................................................................182
The graphical track presentation page ............................................................................................................182
ZOOMING ...............................................................................................................................................................182
SOUND PROPAGATION AND RAY TRACING..............................................................................................................185
WATER CURRENT...................................................................................................................................................185
The posigram control dialogs water current page ...........................................................................................186
Dynamic water current file format ...................................................................................................................186
The posigram windows water current profile menu .........................................................................................187

Figure 110. Posigram window in xy-angle display mode.

The Posigram window presents the temporal and spatial positions of the SED-echoes in a
track. The Posigram is opened when never the system is set up for tracking by one of the
options in the menu: Analysis=Analysis => 1-Setup=Tracking. Additional Posigrams
can be opened from the Analysis => Data insight menu.
The tracker is activated whenever one or more Posigram windows are opened.
The windows have several display modes that can be selected in the Posigram's control
dialog. The most important of modes can be sub-sequent selected by pressing the shift
when the Posigram is active. Each mode presents the track in a specific aspect. To see the
numerical description of the track and the individual echo position, the Track info window

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can be applied.
This window is opened from the Posigrams popup menu or from the main Analysis=Data
insight menu.

As with every window in the sonar program, the following rules apply:
 The window must be activated to respond on keyboard and mouse commands.
 Pressing the right mouse button opens the popup menu.
 F1 gives help
 F2 opens the control dialog

Bottom profile and transducer position

Figure 111 .Menu items controlling the bottom profile and the transducer position

The ZY-exact display mode enables the operator to view the tracks relative to a river or a
lake and not only relative to the sound beam. It can be seen how well the transducer beam
fits the site and whether fish moves close to the bottom or not. The mouse can move and
tilt the transducer to predict the optimal placement at the site. Exact echo positions can be
extracted. See Figure 112.

To display the exact position and the bottom profile correct, the transducer position and
bottom profile must be correctly described. This can be done with the mouse by selecting
in the Posigram or by editing the parameters located in the sonar parameter dialog (chapter
10). Pressing the F7-key opens the dialog as an alternative to using the Utilities
=>Parameter menu. The bottom profile is located in the dialog's environment page while
the transducer placement is located in the dialog's transducer page. Here the parameter:
Opening angle Alo, Opening angle Ath, Pan, Tilt, Dist. center surface and the bottom
profile table has to be set. The parameters involved are colored light blue.

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Drawing a new bottom profile

The bottom profile can be defined simply by drawing the profile in the Posigram window.
Activate the Posigram and press the B-Key. (B is short key to the Draw new menu) Place
the mouse at the first known bottom-profile co-ordinate. The coordinates are displayed in
the Posigram's caption. Press the left mouse button down. Move the mouse to the next
known coordinate and click. Continue moving and clicking until all known coordinates are
defined. Then double click the left mouse button to end the Draw Bottom operation.

Delete the bottom profile

Pressing the Del key or selecting the Delete bottom menu deletes the registered bottom co-
ordinates.

Predicting the optimal transducer position in a river or a lake

It can be difficult to find the optimal position for a transducer in a shallow river or a lake.
If the bottom profile has been measured, playing with the transducer position and water
level on the computer can help finding the optimal placement and tilt. Set the Posigram in
YZ-Exact mode and with the Posigram window activated, press the...
 M-key and then the left mouse button down to move the transducer up and down in the
water and to and from the riverside.
 W-key and then the left mouse button down to adjust the water level
 T-key and then the left mouse button down to tilt the transducer up and down and to
move it to and from the riverside

The keys are short keys to the items in the bottom menu. Playing with the transducer
position can be done without any opened echogram file. Figure 112 shows a transducer
beam tightly fitted to give optimal range without hitting the bottom or the surface.

Edit the bottom profile

This menu item opens the advanced sonar parameter dialog at the environment page. All
the defined bottom coordinates can be seen in the bottom profile table. Coordinates can be
added, edited, saved, loaded and deleted. The values in the grid can be stored in the sonar
file for later use. The profile can also be saved on disk as a special file and loaded into
other files later. See the section: The environment page in chapter 10 for more information
about editing the bottom profile in the grid.

Exporting and importing bottom profiles

Individual bottom profiles are stored within the sonar files. The save and load menus can
export and import the profiles. A profile may be valid for a day or a week before the
transducer is repositioned and the profile is changed. With the save and load menus, the
same profile can be loaded into the wanted files.

Importing bottom profiles during conversion

An alternative way to get the same profile into a set of files is to define the bottom profile
in the survey log applied by the converter. The profile is then described by a keyword
followed by a set of vectors according to the following example:
Bottom_Profile =(-0.82,3.89) (11.12,4.76) (18.20,4.76) (29.99,5.37) (36.78,5.98)
(39.28,5.17)

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Here the numbers within each bracket represent the bottom profile coordinates. The
positions of the numbers within the bracket are 1-range, 2-depth . Units are m. The profile
will be loaded into all files noted after statement until a new Bottom_Profile is
described.
The converters Initial parameter button and template menu provides help to write the
bottom profile into the log. Close any opened sonar file from the main file menu. Define
or load a Bottom profile into the Posigram window. Open the converter for example by
pressing the F12-key. Open the converters second page and select templates from the top
parameter menu. Double clicking on the Bottom_Profile keyword will insert a
Bottom_profile with the defined Bottom vectors into the Survey log. The keyword is
inserted at the cursor's position in the log before the template was opened.

Figure 112. Posigram window in the exact-yz display mode. The surface, beam and bottom
are seen. Tracked echoes from a passing fish are seen near the bottom at Zr=25m.

Copy to clip board

Figure 113. Copy to clip board sub menu.

Submenu for copying graphical and numerical information to the clip board. Use the clip
board to export data to other programs like Excel or Word.

Display modes
The most important display modes can be selected by pressing the Shift key when the
Posigram-window is active. The modes available by pressing the Shift key are:

1. XY-MeterMode: Display the echoes XY positions in meter relative to the transducer.

2. XY-AngleMode : Display the echoes XY positions in angles relative to the transducer.

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3. XZ-MeterMode: Display the echoes XR positions in meters relative to the transducer.

Display also the water current if available and enabled.
4. YZ-MeterMode: Display the echoes YZ positions in meters relative to the transducer.
5. YZ-ExactMode: Display the echoes YZ positions in meters relative to the
environment description found in the Utilities => Parameter application and in the
bottom profile menu. The presentation is meant for horizontal fixed and mobile
surveys. It makes it easy to see how the beam is aligned in the water body, where it hits
bottom or surface and where in the water column targets are detected. Short keys like
the M-key let you move the transducer in and out and up and down relative to the
bottom profile. W-let you move the water level and T changes the tilt.

More modes are available from the control dialog. See Figure 118.

Help
The help menu open the manual at this chapter.

Main pop-up menu

Figure 114. The Posigram's pop-up menu. Press the right mouse button within the
Posigram to see this menu.

Measuring distances

Figure 115. This menu enables the operator to measure distances in the beam.

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Select the ruler to measure distances. Press the R-key, place the mouse at a point in the
window, press the left mouse button down and move the mouse, with the button pressed. A
line will indicate the ruled distance and the caption will display the measured result. The
method measures the distances in the presented aspect. Changing the display mode to
another aspect will change the measured aspect.

Figure 116. Measuring the distance between head and tail of a track in the angular
domain.

Figure 117. Measuring the distance between a track and the bottom in yz-exact mode. The
Euclidean distance and the individual distance along the unit vector are presented in the
caption.

Posigram control dialog

Figure 118. The control dialog is activated by selecting the pop-up menus Control dialog
item or by pressing the F2 -key when the Posigram window is active.

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Main page
Invert +Ath direction.
IF the transducer has been mounted so that the positive athwart angles appear at the
"wrong" side of the Posigram, this checkbox will mirror the measurements.
Use grid.
If checked, a grid will be plotted together with the track.
Connect echoes.
Draws a black line between each echo when checked.
Display mode.
Select the wanted mode by clicking one of the options. With some selections additional
panels will appear presenting more choices.

Track information dialog

Figure 119. The numerical page in the Track information dialog

This dialog presents information about tracked single echo detections. It has two tabbed
pages, one for numerical and one for graphical presentation. The dialog can be opened
from the Posigram window's popup menu (activated by the right mouse button), from the
main menu Analysis => Data insight, or by double clicking a track in a fish basket. (Fish
baskets are not available in Sonar4)

The numerical track presentation page

This page has two options, one for plotting information about each echo in a track, and one
for plotting calculated track features. Selections are done with buttons in the top panel.
To see the track features instead of the echo features, select track features in the radio
group named Show.

Features such as mean track TS, swimming velocity etc. will be presented. The features
and their formulas are described in the section track features and in the section track

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feature equations in chapter 11-System parameter. The dialog described in chapter 11 is

only accessible in Sonar5, but the feature descriptions applie to Sonar4 as well.

Description of the presented echo attributes

Comment Feature Explanation
Time The time when the echo was registered

Relative positions Ath Athwart ship.angle

Alo Along ship. Angle
R range in meters. R is the distance between transducer and target
in meters
TSc Off-axis compensated target strength
TSu Target strength without off-axis compensation.
BC Beam compensation in dB. The difference between TSc and
TSu. (Also called Gain Comp.)
Xr,Yr,Zr Targets position in meter measured relative to the acoustic axis
Exact position Xe,Ye,Ze Targets exact position in meter along the x,y,z co-ordinates.
Assuming that the transducers depth, distance from the river
side (Surface in vert. app.) and the pan and tilt are correctly
described in the Advanced sonar parameter dialog, these values
reflects the exact positions of the detected echoes in the water.
Alo and ath is measured in degree, while all other variables are measured in meters.

The graphical track presentation page

This page displays each echo in a track as a function of time. Select the attribute to plot
and then press the update button to plot the track.

Figure 120. The graphical page in the Track information dialog. See the section: Charts,
in chapter 2 for a general description of the chart.

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Zooming

Figure 121. Sub-menu for zooming in and out.

To zoom in on a particular section, press the Ctrl+Z key or select the Zoom in menu. Then
draw a rectangle around the region to amplify with the mouse. Press the Z key or select the
Zoom out menu to go back to default. Default is defined from the beam opening angles and
the min and max range described in the advanced parameter dialog. Pressing the + / -keys
provides a fast way to zoom in and out. This Zoom function is focused on the center, or the
transducer position depending on the display mode. Pressing the arrow keys will move the
center of the Posigram.

Sound propagation and ray tracing

Figure 122. The last entry on the Posigrams popup menu opens the sound propagation and
ray tracing dialog. See chapter 22 sound propagation for more about this topic.

Water current

Figure 123. Posigram window presenting a track moving against the current. The tracks
direction is seen from the rectangle marking the last echo before the track leaves the beam.

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Current is presented as vectors starting from the acoustic axis pointing along with the
current.
Water current profiles apply basically to horizontal, fixed positioned transducers. When
classifying a track, the track movement relative to the water current can be an important
classification criterion. The program can measure the water current at any range and plot
this information together with the tracks as seen in Figure 123. To display the current
vectors, open the control dialog, select the XZ-meter mode appears and enable the "Show
water current checkbox".

Water current can be defined as static or dynamic. The posigram windows popup menu,
the posigram windows control dialog and the main parameter dialog (Utility => Parameter
=> Bottom Water current profile) handles the two water current definitions.

A static current definition means that the current will be constant throughout one and the
same file. Individual files can have individual profiles and if the file is short relative to the
temporal changes in the current, static profiles may be sufficient in many situations. Static
current profile is stored within each echogram file and can be seen in the main parameter
dialog.

When a static current profile is insufficient and one want to operate with finer current
details, dynamic water current profiles can be applied. As long as the dynamic profile is
not loaded, the static current is used. As soon as the dynamic current is loaded, this profile
will overrule the static current profile. If the dynamic current is cleared with the clear
button, the static current takes over again. Static current is stored in a text file, and must be
loaded into the system from the posigram control dialog. The dynamic current has time
stamps in addition to the current vectors. When SonarX generates a track the current
profile closest in time to that track will be presented.

The posigram control dialogs water current page

Figure 124. The Posigram control dialog’s water current page. The page does only apply
when the posigram is in XZ-mode.

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Show water current checkbox

To se any current profile in the posigram window, this checkbox must be checked.
Water current vector gain
Water current is defined as vectors. The current gain is a factor adjusting the visual length
of the current indicators. See Figure 125.
Load button and time window
This button will open a file open dialog. Select a prepared ascii text file containing the
current profile here. If a current profile has been loaded, the label
Show current within a time window of 60 seconds will appear. This means that each time a
track is defined, a window of +- 60 seconds is placed around the track time and all current
registrations found within this time window will be presented. 60 second is here just an
example. The value can be defined by the user.
Clear button
Pressing this button will clear the dynamic water profile from memory and set the system
to use the static current profile.

Dynamic water current file format

The following rules go for the dynamic water current profile text file. The sign “|” means
tabulator. Semi-column as the first sign on a line after line 4 means that the line is a
comment. Line 1:, Line 2: is used here in the text to indicate line numbers, and is not to be
found in the actual current file.

Line 1: Free comment, header or whatever

Line 2: Code | 121461 This is a code that must be written exactly as defined
here.
Line 3: Version | 1 1 Must be found in the second column. The text
“version” in the first column is not used.
Line 4: dd.mm.yyyy | hh:mm:ss | z (m) | Vx(m/s) | Vy (m/s) | Vz(m/s)
This is a header line Note the date and time format
Line 5: 04.03.2005 | 10:27:30 | 25 | 1 | 0.4 | 0.1 First
data line
Line 6: 04.03.2005 | 10:27:35 | 15 | 0.7 | 0.4 | 0.1 Second
data line
:
:

No text without a leading semi column can be placed on lines after the last data line. Text
can, however, be applied in columns after the last column defined in the format.

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The posigram windows water current profile menu

Figure 125. Water current profile menu. The menu is enabled when the Posigram is in the
XZ-mode (Bird view) in a horizontal application.
Add track as current
First track the echoes from the drifting targets in the echogram-window. Then activate the
Posigram window and press the Alt+A-key. The current vector will be displayed in the
caption and plotted in the diagram. Alt+A-key is the short key to the pop-up menus Current
profile -Add track as current. Artificial target can be thrown into the river at different
ranges to get reliable tracks at all ranges.
Draw current manually
This menu option let the operator draw the current vector manually with the mouse.
Activate the Posigram and press the Alt+M-key. Then position the mouse at the range
where the current is known. Press the left mouse button down and move the mouse in the
direction of the current. The caption displays the current speed. Let the mouse up when the
current is correct. Repress the M key to define a new current vector.
Edit current profile table
This menu item opens the advanced sonar parameter dialog at the environment page. All
the defined water current vectors can be seen in the water current table. New current
vectors can be added and old vectors can be edited or deleted. The water current values
seen in the grid will be stored together with the sonar file when the file is closed. The
profile can also be saved on disk as a special file and loaded into other files later. See the
section: The environment page in chapter 10 for more information about editing the current
vectors in the grid.

Save
The save button can save the static current to a disk file.
Load
The load button can load a static current from a disk file.

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Main menu

ABOUT SONAR PARAMETERS .................................................................................................................................239

THE TOP MENU.......................................................................................................................................................240
Parameter_files ................................................................................................................................................240
Edit ...................................................................................................................................................................241
Export...............................................................................................................................................................241
Apply to all menu .............................................................................................................................................241
Apply menu.......................................................................................................................................................241
Close menu .......................................................................................................................................................242
Help menu ........................................................................................................................................................242
PARAMETER DIALOG PAGES ...................................................................................................................................242
Information page ..............................................................................................................................................242
Calibration parameter page .............................................................................................................................244
SED page .........................................................................................................................................................246
Amp echogram page.........................................................................................................................................247
The application page ........................................................................................................................................248
Platforms ..........................................................................................................................................................228
Transducer platform (T) ...................................................................................................................................229
Base platform(B) ..............................................................................................................................................229
World platform and GIS ...................................................................................................................................229
Sensor page ......................................................................................................................................................229
Horizontal profiles page ..................................................................................................................................229
Echogram parameter page ...............................................................................................................................229
System info. page..............................................................................................................................................230
DISABLED AND ENABLED PARAMETERS .................................................................................................................230
PARAMETER COLORS .............................................................................................................................................231
Colors applied when preparing for conversion ...............................................................................................231
Colors applied for post-processing of converted files ......................................................................................180
Meaning of colors ............................................................................................................................................181

About sonar parameters

See also the section Parameters in chapter 2.
Sonar parameters are numbers and text related to each recorded sonar file. Some are
important for calculations while others provide information only. SonarX uses more than
70 different parameters.

When an echogram file is recorded in the field, the operator may set calibration parameter
such as gain and environmental parameters such as the absorption coefficient. The
parameters are not always stored in the recorded files. Simrad's EY500/EK500 stores
parameters only if the operator turns on the parameter enter telegram and actively enters or
request that parameter during the recording. Since post-processing depends on these
parameters, the operator has to deal with them.

Parameters can be handled two different places in the program.

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1) The parameter dialog described in this chapter gives access to all available parameters.
In addition to calibration and single echo detection parameters, parameters such as
transducer placement and application information can be described. The dialog can be
opened before a conversion is started to describe the file to be converted. After conversion
the dialog can be opened to give information about the converted file. These two situations
differ and the dialog will behave slightly different. Some menus will be disabled in one
situation and other in the other situation.

2) The converter dialog. The second page in the converter has tools for writing a survey
log. The log can describe the involved parameters for individual files. Parameters stated in
the converters survey log will overwrite parameters in the parameter dialog.

For more information about parameters, see for example the sections: The surveylog and
individual parameter settings, Sonar parameters and keywords, and List of parameter
keywords in chapter 5.

The top menu

The parameter dialog can be opened to set initial parameters before conversion of a new
file or it can be opened to get information about a converted file. The dialog will behave
slightly different, in the two situations, and different menu items will be invisible or
disabled. The caption will indicate whether the dialog was opened to prepare conversion or
to give information about an open file.

Parameter_files

Save parameters
Parameters can be saved as global or local templates. Global templates are saved in the
program folders subfolder named default, while local templates are saved in the working
folder. The program will suggest a filename composed by the selected converter and the
text found written in the transducer type edit box. The operator may, however, name the
file with another name. In this way it is possible to build up a library of the operator’s
favorite transducers and applications.
Load parameters
Let the operator select templates to load into the system as initial parameters. This menu
items are disabled during read operation. Note that parameters with the “take from source
file” color must be dbl. clicked to indicate that the loaded parameter should overrule the
parameter in the source file.

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Load calibration data from ascii file.

The system will ask for an ascii file from the systems current working folder. The file must
follow Simrad’s EK60 ascii based calibration file standard. The menu is only enabled
during conversion and loads parameters into the calibration page only. If successfully
loaded, all parameters on this page will change colors to indicate that the parameters are
taken from the dialog and not from the source file.
Invert parameter colors
This menu will turn of all the “take parameter from file” colors if on and vice versa.

Edit

Add explanation
This is a check menu. If checked the copy to clipboard menu will contain additional
explaining information
Set parameters to default
This set all parameters to the programmer’s favorite values. Calibration parameters will not
be set during read operations.
Change MGC
Max gain comp is applied in the beam volume calculation algorithms. If SED has been
detected without MGC restrictions one may want to study the resulting SED position
distribution and change MGC according to the results. The system will guide the operator
in these special situations.

Export
Selected parameters from all opened files
If one have opened let say 5 files in the advanced file open menu one may want to export a
set of selected parameters from all of them. The menu item opens a parameter selection
dialog, and then writes the selected parameters to clip board or file.
All parameters from this file
Write all available parameters to clipboard or file.

Apply to all menu

This menu option is only visible when the parameter dialog is opened for already
converted files. When preparing conversion this menu item is not visible. Pressing “Apply
to all” will update not protected parameters to all files in a working folder. Examples of not
protected parameters are Survey, operator, bottom profile water temperature etc. File name
and most calibration parameters are protected and will not be updated.

Apply menu
Updates the internal parameters from the dialog without closing the dialog

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Close menu
Closed the dialog without updating the internal parameters from the dialog

Help menu
Opens this chapter

Parameter dialog pages

The advanced parameter dialog gives the operator insight in all the involved parameters.
Here all the parameters controlled by the simple parameter dialog are redefined together
with parameters controlling the less important functions and the read only parameters
displaying information extracted by the converter. See the section List of parameter
keywords in chapter 5.
Sonar parameters are divided in four groups. Each group is organized in a tabulated page.
The dialog is opened from the programs top menu: Utilities = Sonar parameter. The
importance of the parameters and their functions is seen from their colors as described for
the basic parameter dialog.

Information page

Figure 126. Information page

This page contains text and picture information.
Survey
Free text string of 60 characters describing the Survey. (Or what ever is needed). The
string is displayed in the advanced file open dialog to help the operator to open the correct
file. When opened, the string is seen in the program's caption.
Transect
Free text string of 60 characters describing the transect. (Or what ever is needed) The
string is displayed in the advanced file open dialog to help the operator to open the correct
file. When opened, the string is seen in the program's caption.
Rec. Nr.
When files are converted, the converter assigns an individual number to each file. The
number is seen in the advanced file open dialog and in the main program's caption. With
many files to analyze in one folder it may be convenient to identify the files by a simple

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number. Changing the number is legal.

Operator
Free text string of 40 characters indicating a person responsible for the original recording.
(Or what ever is needed)
Picture file
Name of a digital picture or a drawing in jpg format. The picture is displayed in the upper
left corner of the dialog framed by Splitters. Use the splitters to resize the picture. Digital
cameras, scanners or programs like Paint can produce pictures. The picture file must be
stored in the same folder as the converted sonar file or in the Super folder. Different sonar
files can refer to the same picture file name. The image browser button launches the image
browser program if installed. This program shows all the available pictures in the working
folder. It can also convert picture files from bitmap to jpg.
Text file
Name of a text file. The file is presented in the dialogs lower memo where it can be read
and edited. The text file is also displayed in the advanced file open dialog to help the
operator to open the correct file. The text filename can be individual for each sonar file or
common for many files. The actual file must be located in the same folder as the sonar file,
one of it's super folders, in the program / default folder. The file is a plain text file and any
text editors capable of saving plain text can edit it.

When the converter converts a sonar file, it produces this text file by default. The text file
are given the same name as the sonar file, but the extension will be ".txt" The text file will
contain information extracted from the converters survey log.

To force the converter to use a special filename, add the text line:

Text_File = MyName.txt

in the converters survey log or in the parameter dialog. See the section Survey log in
chapter 5 for more information.
A different file can be attached later simply by typing the filename into this dialog's Text
file edit box or by pressing the browse button behind.

Note that it is legal to add text and notes while working with the converted files.
Browse buttons
Use the browse buttons to see the available pictures and text files and to change the file
names.

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Calibration parameter page

Figure 127. The calibration parameter page. In this case all parameters will be extracted
from the source fileexcept for the alpha witch has been double clicked . Doubleclicking a
parameter gives the operator control of the parameter. This dialog is dedicated to a
specific echosounder and will look different for other echosounders. For Sonar4 the
transducer panel will contain the transducer depth as well. See Transducer depth in the
Application page section.
3dB beam width.
Defines the opening angles of the sound beam measured at a -3dB level. The parameters
control the presentation of the beam in the position diagram window. They are also
involved in the biomass estimation.
Angle sense
Angle sense describes the relation between the electrical and mechanical degrees in the
transducer. The converter needs the parameters when the built-in single echo detectors or
the Crossfilter detector is applied.
Angle offset
Angle offset describes the offset between the actual and measured acoustic axis. The
converter needs the parameters when the built-in single echo detector or the Crossfilter
detector is activated.
Equivalent beam angle
Ideal opening angle applied in the sonar equation for volume reverberation (Sv).
TS-transducer gain
Amplification factor applied in the single target sonar equation applied when sample data
is converted.
SV-transducer gain
Amplification factor applied in the sonar equation for volume reverberation (Sv).
Power
Power is the transmitted power in watt. Different transducers and echo sounders have
different values. Power is involved in the conversion of sample data.

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Pulse-width
Duration of the transmitted pulse measured in ms. This parameter is important for
conversion single echo detection and biomass estimation.
Frequency
Frequency of the transmitted pulse measured in kHz. The parameter is important for
conversion of sample data and for biomass estimation
Band width
Band width means the transceivers band with. This parameter is needed to find the correct
correction factors for EY500 and EK500. These sounders register the band with as short
medium and wide. The real values are found from the table accessed by the help button.
Transducer type
Free text string applied as information to the operator.
Reg nr
Free text string applied as information for the operator.
Temperature
See the calculate button below.
Salinity
See the calculate button below.
Alpha.
Absorption coefficient.
Soundspeed.
Speed of the sound in the water

Dynamic sound and alpha profile button

This button opens an information message about how to apply dynamic sound profile and
alpha correction. This is at the moment done through the Analysis/Pre-analysis /Dynamic
sound profile correction menu. Correction and profiles are applied to files after they have
been converted.
Calculate buttons.
This buttons opens a dialog for calculating the sound speed and absorption coefficient.
(Francois and Garrison 1982) and

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SED page

Figure 128. SED page

Detector panel
This panel contains the actual detector. Echoes with similar echo length as the transmitted
pulse is assumed to be echoes from single targets.
Min echo length
is the minimum accepted duration of the received echo pulse measured relative to
transmitted pulse. The Single echo detector does not accept pulses shorter than this
parameter value. The echo length is measured 6dB below the peak.
Max echo length
is the maximum accepted duration of the received echo pulse measured relative to
transmitted pulse. The Single echo detector does not accept pulses longer than this
parameter value. The echo length is measured 6dB below the peak.
Evaluator panel
When an echo has been detected, it is evaluated according to a set of criteria. The echo has
to pass all the criteria to be accepted.
Min target size
Min target size is the same as Simrads single echo detectors Min value. The threshold
rejects all single echo detections with off-axis compensated target strength below this
threshold. Higher thresholds can be set in the echogram control dialog but not lower.
Max phase dev.
An echo pulse may consist of one or few samples. The angular position is calculated from
the mean values of these samples. If the standard deviation within the samples is too high,
the echo will not be accepted as a reliable single echo. With two angular domains, two
standard deviations are calculated. The larger of the two is compared with the Max. phase
dev. parameter. Note that EY500 and EK500 operate with internal electrical phase steps
while SonarX operate with true mechanical angles when testing the standard deviation.
Conversion calculations and a conversion table are found the section Single echo detection
in chapter 4.
Multiple peaks suppress.
This parameter enables suppression of multiple peaked echoes. Off, medium and strong are

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the options. Strong rejects all echoes with multiple peaks while medium demands a local
dip of 1.5 dB between peaks before rejecting the echo.

Beam clipping panel

The beam clipper cuts the SED beam into a define shape and size. Two options are
available, round and rectangular. For an elliptical transducer, round means elliptical, while
for a circular transducer round means circular. The Max. gain. comp. parameter will be
seen if round is selected. If rectangular is selected, parameters for defining the size of the
rectangular beam will be seen. A round beam is the normal and the default. Rectangular
beams may have advantages for tracking in that it gives a greater chance to obtain same
track length on the sides of the beam as in the middle. Note that the fundamental beam and
its sensitivity can not be changed. This means that a rectangular beam will have a variable
sensitivity along the edges. The corners will have lowest sensitivity and thereby lowest
target detection probability. This must be considered if rectangular beams are applied.

Max gain comp.

When beam clipping is set to round, the max. gain. comp. parameter is visible. Echoes with
higher off-axis gain compensation than this parameter will not be accepted. If set to 3 dB,
all echoes outside the -3 dB beam (half beam) will be rejected.
Min and max beam angle edit boxes
When a rectangular beam is selected, the appearing panel will contain edit boxes for the
min. and max. opening angles. Pressing the def. (default) button will set the rectangle to
the angles noted by the -3 dB opening angle parameters (half beam angles) located in the
calibration page.

Figure 129. Parameters for defining the rectangular beam appear when rectangular is
selected.

Quality button
This button will open the quality definition dialog to display the applied quality definition.
Normally this definition will be equal to the parameters set in the single echo detector. The
Echo length single echo detector and the Crossfilter single echo detector located in the
Analysis => Pre-analysis menu, and the echogram control dialogs quality page uses the
quality definition. The button will not be seen when the parameter dialog is opened from
the converter.

Amp echogram page

This page contains parameters important to the converter during conversion.

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Base threshold
is the lowest echo intensity that will be extracted from the original source file during the
conversion. This parameter can not be changed after conversion. While reading of files
thresholds can be altered in the echogram control dialog. See section Thresholds in chapter
7 for more information.
Range resolution
is normally found from the source file or taken from default tables. The operator may,
however, double click this parameter and take control. The take control option was
implemented to enable using a few special designed EK500 echo sounders with non
standard range resolution.

The application page

Figure 130. Application main page

The page describes parameters related to the application, transducer placement, motion
sensors etc. The information given here is important for biomass estimation and for target
position estimation. Biomass estimation needs to know the alignment of the beam to find
the surface area and the surface density. For tracked targets, the information is needed to
be able to estimate the correct target position and depth.

Application selector
Do always select the application before adjusting any other parameters on this page. The
meaning of the parameters will change depending on the selections.

Platforms
There are three platforms. The Transducer platform describes the transducers aiming and
orientation relative to the Base platforms xyz-coordinate system. The Base platform is a

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local reference point for the survey and describes the distance to the transducer platform
while the World platform relates the Base platform to the world.

Transducer platform (T)

e) Pan, f) tilt and g) rotation.
Set the transducers alignment and aiming. The letters e, f and g are seen in the application
picture explaining the meaning and what coordinates they work along. For fixed
applications these parameters can be connected to the motion sensors. This is done by
selecting sensors on the sensor page. Whether a parameter is controlled by a sensor or not
is indicated by the parameters color. Grey color indicates that the sensor has control.
+Alo and ath direction
The split beam transducer obtains the angular positions in +/- degrees. It depends on the
transducer mounting whether up or down, upstream, or downstream, for and aft, port and
starboard will be + or -. These settings are used to estimate correct position of tracked
targets in the water body.

Use water current labels checkbox.

The checkbox is only visible in fixed position applications. It changes labels e.g. from left
right to upstream downstream.

Base platform(B)
The base platform is a local reference point keeping track of where the transducers are
placed.
This makes it possible to obtain comparable track statistics during a long period when the
transducer platform has to be moved around.

The parameter a, b and c describes the transducers position relative to the base platforms
xyz- coordinate system as shown in the application pictures.
abc parameters
Meaning of (a) The transducer platform is moved a meter along the x-axis.
Meaning of (b) The transducer platform is moved b meter along the y-axis.
Meaning of (c) The transducer platform is moved c meter along the z-axis.

For horizontal fixed applications, x-axis points downstream or down the shore, y-axis up
and z-axis normal to the shore-line. For horizontal mobile applications x is forward, y is up
and z is out from the boat in the direction selected with the transducer aiming selector
which can be starboard (right) or port (left). Note that depth will be along the -y-axis. Note
also that when the base platform is placed onboard a mobile boat or fleet, x, y and z-axis
will be pointing the way the boat goes as long as motion sensors are not applied for
compensation. With out motion sensors y will not be vertical but point up along with the
mast wherever that will be if there are waves.

For vertical applications, x is the same as for horizontal, while y and z-axis is exchanged.
This is so because we have let the z-axis be defined from then acoustic axis.

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Add (c) to range in echogram checkbox

The base platforms c parameter describes the transducer displacement along the z-axis. For
vertical applications this will be the transducer depth and for horizontal applications it will
be the distance from the shore. When checked on, c will be added to the range in the
echogram. If the transducers tilt and pan are not too high the range seen in the echogram
will indicate the actual depth or the actual distance away from the shore.

Water level
This parameter is only visible for horizontal fixed applications and indicates the distance
from the base platforms height down to the water. The parameter is used by the system to
find the targets depth. If the base platform is placed, let say 1 meter above the surface of a
lake and the transducer is placed 2 meter below the surface, the vertical distance (b)
between the base platform and the transducer is 3 meter. Water level is then 1 meter which
is subtracted from the depth estimates to find the depth relative to the surface and not
relative to the Base platform. If the base platform is positioned in level with the surface,
the water level parameter should be 0.

World platform and GIS

This panel relates the local base platform with the World and enables estimation of the
targets GPS positions. For fixed applications, the operator must type in the GPS position of
the Base platform and the direction of the x-axis rel. north. For mobile applications,
position and heading is taken from the GPS signal. It is assumed that the GPS receiver is
placed at the center of the base platform. Targets described by geographical positions and
altitude below sea level can be exported to geographical information systems (GIS)

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Sensor page

Figure 131. Sensor page with selector is located on the Application’s sensor page. The
names on the sensor selector list will reflect the echosounder manufacurers names but may
contain different sensors than planned by the manufacturer. The selectors enable the
operator to connect whatever sensor to the echosounder.
The application page has, in addition to the main page, a sensor page. Sensors for pan, tilt,
rotation, pitch heave and roll can be connected to the system. It depends on the selected
application how the sensor information will be used. When fixed location application is
selected, the sensors can be connected to the transducers d) pan, e) tilt and f) rotation as
seen in Figure 131. If mobile application is selected, these labels will change into pitch,
roll and heave. The labels indicate what they will be applied for in Sonar X.

Sensor connection panel

As long as the sensor selectors state “Not connected“ the static parameter value seen in the
main page will be used. If sensors are available, they can be selected with the sensor
selectors. Only the operator know the sensors and how they where mounted. The names
available in the sensor selectors (not seen in the figure above) will be the same as found in
the actual echo sounder manual. As soon as sensor has been connected to a parameter, the
output from the sensor will take over for the static parameter. For d) tilt, in a fixed
horizontal application, features such as the depth of a passing fish will be estimated based
on the sensor output for the actual ping and not from the fixed tilt setting. Hence, even if
the transducer is slowly tilted more and more down while a fish is passing in a horizontal
application, the fish trajectory and position in the water column will be correct estimated.

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The offset, factors and inverter parameters are used for sensor calibration.
Plotting sensor output
The chart in the bottom of the sensor page can plot the output from the sensors versus ping.
The chart can show the output for the visible part of the echogram, or the output for the
entire file. When visible part is selected, the chart will show the sensor output for the
pings presented in the echogram.
How to apply sensor data
Various sensors can be mounted on the transducer, platform or on the boat and connected
either directly to the echo sounder or to the PC through one of the PC ports. Simrad and
DIDSON store the sensor data directly in the source file while BioSonics store the sensor
data in separate files. Sensor data stored in source files will be extracted automatically
during conversion, while data stored in separate files can be imported with the import
button located on the Sensor page.
Importing sensor data from BioSonics
BioSonics echo sounders store sensor data in files with extension .hrp. These files must be
converted to .csv files with the program named hpr2csv.exe available from BioSonics. The
program produces csv files that can be read both by Sonar X’s import routine and by
Excel.

Horizontal profiles page

Figure 132. Hor profiles page

Bottom profile panel
This bottom profile is the profile found under a fixed, horizontally aligned transducer and
not the bottom line seen with a vertically aligned moving transducer. The bottom profile is
presented and handled in the position diagram window, while the bottom line is presented
and handled in the echogram window. When the position diagram edits the profile, it is the
value seen in this grid that is being changed. Editing the values directly in the grid is legal.
The bottom profile is defined by a set of range / depth coordinates.

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The bottom profile is plotted in the position diagram window's Exact YZ-mode. The
profile enables the operator to see the sound beam and the detected targets relative to the
bottom and surface in a shallow river.
A separate bottom profile is stored in each sonar file. Hence different profiles can be
applied throughout a long-term survey where the transducer might be repositioned.
See the section Bottom profile in chapter 9 for more information.
Water current profile
The water current direction and strength is important for classification of fish tracks in a
river. By seeing the current and the track together, it is easy to verify whether the track is
drifting or moving actively. The water current grid stores the vectors presented in the
position diagram. In the position diagram the vectors can be displayed as red lines starting
from the acoustic axis at different rages. Tools for handling the current vectors are also
found in the position diagram. It is, however, this grid that maintains the vectors. Editing
directly in the grid is legal. The Range and the X, and Z component has to be entered while
the speed is calculated automatically. X is the velocity component 90 deg. to the acoustic
axis while Z is the component along the acoustic axis.
See the section Water current profiles in chapter 9 describing the Position diagram
window.
Sound profile panel
Under construction.

Echogram parameter page

Figure 133. Echogram information page

This page is visible only during read operation and not during conversion. It contains
information about the echograms extracted during conversion.

Echogram info panels

These panels contain min and max information such as min and max TS etc.

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TVG and Sonar equation

The Amp echogram panel in Figure 133 displays both the TVG and the applied sonar
equation. A TVG of 40 log R are normally associated with the sonar equation for the point
source model, while a 20 log R TVG is associated with the sonar equation for volume
reverberation. This is however, only true if we assume spherical spreading of the sound. In
shallow water, cylindrical spreading may be a more appropriate model. Thus, there are
situations where the TVG may differ from the traditional 20 and 40 log R. SonarX handles
this by operating with independent models and TVG settings.

For details about the models and calculations, see the section sonar equations and
conversion between TS and Sv, in chapter 5.
Amp echogram info panel
This panel gives information about min and max sample values detected in the Amp
echogram. The parameters are detected automatically by the converter.
 Intensity presents the lowest and highest TS or Sv value obtained in the file.
 Range presents the shortest and longest range obtained in the Amp and SED echogram.
The values control the auto range function and the operator can change it.
 Meter per sample presents the distance between each sample in the Amp echogram.
This is also described as the range resolution.
 Number of samples in ping: The total number of samples in each ping in the Amp
echogram.

SED info panel

The SED panel gives information about the min. and max. values detected in the SED
echogram. The parameters are detected automatically by the converter.
 TS present the lowest and highest target strength in the file. The values control the
base threshold and the auto color step functions in the echogram control dialog (chapter
7).
 Range present the shortest and longest range obtained in the Amp and SED echogram.
The values control the auto range functions in the echogram control dialog (chapter 7).
 Athwart ship presents the min. and max athwart-ship angles obtained in the SED-
beam.
 Along ship presents the min. and max along-ship angles obtained in the SED-beam.

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System info. page

Like the Echogram info page, the system info page is only visible during read operation. It
contains additional information about the system and the conversion.

Disabled and enabled parameters

Parameters involved in the conversion can not be changed later and will be disabled during
post processing. It will not help to change them since they already have been used eg. to
calculate the TS or Sv. To change disabled parameters, re-conversion is necessary.

Parameter colors
Colors are used to inform the operator about the parameters importance ands use. The
parameter dialog can be opened ether before a conversion to describe the files to be
converted or later to give information about converted files. Two different set of colors are
applied. The meaning is seen in the parameter dialog’s definition page (Figure 134).

Colors applied when preparing for conversion

During conversion, the parameter color indicates whether the parameter will be taken from
a) the source file. b) the parameter dialog or file log.

 If a parameter has the important, used or not used color (Figure 134.), the
parameter will be taken from the parameter dialog or from the converters survey
log if the parameter is noted there.

 If a parameter has the “Extract from echogram source file” color, the value will be
taken from the source file and not from any other places. Not even from the
converters file log if it is referred there.

 Double clicking a parameter will, if the parameter exists in the echosounder source
file, switch the color between the “Extract from echogram source file” color, and
one of the important, used or not used colors seen in Figure 134.

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Colors applied for post-processing of converted files

Many parameters that were important before conversion will be disabled during post-
processing. To change these parameters the source file has to be re converted with correct
parameter setting.

Meaning of colors
Important color
Parameters with the important color must be set before the conversion. These parameters
will be directly involved in the conversion e.g to calculate Sv ond TS.
Used color
Parameters with the used color can be set before conversion or later during post
processing. Examples are parameters such as transducer orientation and placement, water
current and bottom profile. These settings will not influence on the conversion. They may
or may not be important later during post-processing, but the operator does not have to
bother about these parameters during conversion if he knows they don’t matter or want to
set them later.
Information color
Parameters with the information color are not used by SonarX. Still it may have meaning
to know for the current operator to know e.g. who recorded the file, the file number and so
on.
Disabled parameters
Parameters with the disabled color should not be changed. It is for example meaningless to
alter the transducer gain during the post processing. If the gain was set wrong during the
conversion, the file should be reconverted.
Error color
If a parameter is typed erroneously, the parameter will turn into this color. It may be that a
letter has been typed where a number is expected, that a comma is used where a dot is
expected or that the value is out of range.

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Figure 134. The definition page holds the colors and axis definitions. The convert panel is
valid when preparing conversions while the read panel is valid during post processing of
converted files.

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SONAR5

Most of the remaining part of the manual describes methods found in Sonar5 only.
Exceptions are the feature description in chapter 11 and the simple tracking description in
chapter 12.

Balk and Lindem 259

11 System configuration dialog
Main menu

ABOUT ............................................................................................................................................................. 262

OVERVIEW ....................................................................................................................................................... 262
GENERAL PAGE ................................................................................................................................................ 262
Single echo quality panel ........................................................................................................................... 262
Decimals and GPS ..................................................................................................................................... 263
Export options for fish baskets ................................................................................................................... 263
Auto exports panel ..................................................................................................................................... 264
Echo integration of erased data ................................................................................................................. 265
TRACK PAGE .................................................................................................................................................... 266
TRACK FEATURE OPTIONS PAGE....................................................................................................................... 267
TS features panel ........................................................................................................................................ 267
Apect angle panel ....................................................................................................................................... 267
TRACK FEATURE LIBRARY PAGE ...................................................................................................................... 268
SPECIES PAGE .................................................................................................................................................. 269
SPECIES SELECTOR AND CALCULATOR PAGE .................................................................................................... 270
Species selection ........................................................................................................................................ 270
Calculator .................................................................................................................................................. 270
SPECIES DATABASE PAGE ................................................................................................................................. 271
Editing the database................................................................................................................................... 271
Save and load, export and import to and from spreadsheets ..................................................................... 271
Pictures and text files ................................................................................................................................. 272
Meaning of the columns in the species database........................................................................................ 272
CATCH BASKET PAGE ....................................................................................................................................... 273
Principles ................................................................................................................................................... 273
Estimating length and weight of tracked fish by Catch basket ................................................................... 273
Biomass estimation based on catch data .................................................................................................... 274
Converting biomass estimation result into weight by Catch basket ........................................................... 274
Scaling the biomass result into species and size proportion by Catch basket............................................ 274
Using the Catch basket dialog ................................................................................................................... 274
Edit Catch basket with other spreadsheet programs .................................................................................. 275
Catch basket file format ............................................................................................................................. 275
TRACK FEATURE DESCRIPTION ........................................................................................................................ 276
Size features ............................................................................................................................................... 276
Track echo-features.................................................................................................................................... 279
Position features ........................................................................................................................................ 279
Track distance-features .............................................................................................................................. 281
Velocity-features ........................................................................................................................................ 282
Track behavior-features ............................................................................................................................. 283
Track quality .............................................................................................................................................. 287
Image tracking-features ............................................................................................................................. 287
Features obtained by combining the SED and the Amp echogram ............................................................ 288
TS, LENGTH AND WEIGHT CONVERSION ........................................................................................................... 290
TS length conversion .................................................................................................................................. 290
Length to weigh .......................................................................................................................................... 291
Multiple species conversion ....................................................................................................................... 291

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About
The system configuration dialog is only available for Sonar5-Pro. The dialog controls the
behavior of the program, what to display, and how to perform calculations. It also contains
the species size calculator, the species database and the catch basket.

The settings are automatically stored in the configuration file(.cfg) in the same folder as
where the SonarX.exe file is located. It is stored each time SonarX is closed. Thus, the
program will remember the last applied setting. Figure 135 present the dialogs pages.

The system configuration dialog is accessed from the main menu: Utilities-System
configuration or by its short-key F9. Double clicking a line in the track feature list box in
the classification window or selecting track feature library menu in the fish basket will also
open this dialog. (See chapter 13 and 14 respectively)

Overview

Figure 135. System configuration dialog's selector page.

When the system configuration dialog is opened by pressing F9 or y the Utilities =>System
menu it will start by showing the overview page from where one can select among the
described topics. The text in indicate the content of each topic. To select a topic, click on
the topic button.
Ok button
Accept the settings and close the dialog.
Help
Opens this chapter in the manual.

General page
Single echo quality panel
An echo with echo length close to the transmitted pulse length, with stable phase, with
position located within the 3dB beam and with one single peak can be said to be a high
quality echo. SonarX enable the operator to define quality according to the mentioned
criteria. In low signal to noise ratio (SNR) situations, few echoes are of high quality. For

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tracking we need as much detections as possible from each target. For track size, position
and velocity estimates we need high quality. Hence, it is convenient to let the system detect
as many echoes from a track as possible and mark them according to a quality definition.
The system can then use all echoes for tracking and the high quality echoes for sensible
track feature estimations.

The converter marks all single echo detections with high quality.

Quality definition is applied in two ways after conversion:

 when the single echo detectors located in the Analysis => Pre-analysis menu are
applied
 When then the Redefine button in the system configuration dialog is pressed.
Do not apply low quality echoes in analysis checkbox
Echoes marked with low quality can be kept out of sensible estimates by checking the “Do
not apply low quality echoes in analysis” checkbox

Redefine quality button

This button will close the system configuration dialog and open the echogram control
dialog’s quality page. This page will be set up for redefinition of quality. See the echogram
control dialogs quality page in chapter 7.

It will depend on the available echogram data how well the quality can be redefined. The
most accurate definition is applied if the Amp-echogram has high resolution and low base
threshold and when the phase file is available. If not the algorithm will still do its best but
lack of information will influence the result.

Erase low quality echoes button

This button will close the system configuration dialog and open the echogram control
dialog’s quality page. This page will be set up for erasing echoes according to quality. See
the echogram control dialogs quality page in chapter 7.

See also the echogram control dialogs noise page in chapter 7 about erasing and recalling
echoes.

Decimals and GPS

Controls the decimals for various values, decimal separator and GPS options.

Export options for fish baskets

Controls what to include and what to export from a fish basket.

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Auto exports panel

Checking Auto Export on will open a panel with a set of export options. These were
originally implemented for the Remote Control system, but have proved useful in many
other situations as well. It enables for example export of individual single echo detections
when a biomass estimation analysis is carried out. Note that for these exports to occur, the
appropriate analysis must have been applied. Tracking results will naturally only be
exported if the system is set up for tracking. The analyzer I and II control dialogs has status
indicators that will indicate whenever this export is turned on or not. Most methods are
only activated from the Analysis controller II.

Biomass basket
If checked on, and if the system is set up for biomass analysis, then this auto export
function will force the biomass analysis to export result files in the checked format. (.bio)
is the biomass baskets binary format.) Both .bio and .txt can be checked simultaneously.
If Clear is not checked on, the results will pile up in the biomass basket upon sucessive
analysis.

Biomass result grid.

The results seen in the biomass windows result grid will be exported to text files.

Events exported as text

If there are events in an analysis cell name and details about the events will be exported to
a separate text file.

Fish baskets
Same as for Biomass baskets. If checked on, tracked results will be exported.

Compressed echograms as .jpg

While analyzing files, the system will compress the echograms and take pictures. The
echogram pictures are saved as jpg pictures.

Single Echo detection information

A text file will be generated for each analyzed echogram file. The file will contain rows
with single echo detection information together with information about which analysis cell
they belong to. The threshold edit box defines the lowest TS value that will be included in
the table.

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Echo integration of erased data

Erasing noise in recorded data may be necessary, but it may also influence on the
abundance and biomass estimation results. If not done correct, one may end up with a
dataset with much higher or lower density of targets relative to actual density. For example
if all regions with very low density of fish are regarded as not recorded, then the remaining
data will contain a very high density of fish. Some kind of noise occurs in regions with low
density of targets, while other kinds of noise may be seen independently of the densities of
interest.

Options:
1) Erased data is regarded as NOT recorded
2) Erased data is regarded as thresholded
3) Erased and Thresholded data is regarded as not Recorded

Option 1:
Option 1 is the default option. Rising air bubbles, disturbance from a second echo sounder,
electric noise etc do often occur randomly in layers in your data. It is reasonable to believe
that this kind of noise occur random without any preference for hiding e.g fish echoes.

Option 2:
Option 2 is recommended when one assume that the erased data systematically contain less
targets than the remaining data. For example if zoo plankton is to be analyzed and fish is
the noise that are erased, then option 2 is correct if one assume that there are less plankton
keep away from the fish.

Option 3:
Option 3 is rarely used. It is related to special situations concerning target frequency
function studies.

How it works:
Consider the mean Sv obtained from an analysis cell in the amp echogram.

 1 
MeanSV dB   10 log 10 Sv ( dB ) i / 10 
M 
 i 

where index “i” runs over all samples in the selected region of the echogram except
 Threshold samples
 erased samples.

Normally in averaging, M would have been the involved number of elements in an

averaging. Here M is controlled by the three options.
 Option 1: M= Total number of samples in the analysis cell - erased samples
 Option 2: M= Total number of samples in the analysis cell

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 Option 3: M= Total number of samples in the analysis cell - erased samples -

thresholded samples

This can be demonstrated with the following formulas:

P2
 R2i  R1i 
M1    R
 Erased i 

i  P1
P2
 R2i  R1i 
M2    R 

i  P1
P2
 R2i  R1i 
M3    R
 Thresholded i  Erased i 

i  P1

where index i is the ping number index running between the ping borders in the analysis
cell (P1 to P2). R is the range resolution measured in meters per sample, R2i-R1i is the
analyzed range for each individual ping. R2i, R1i may be the upper and lower boundary in
an analysis cell, but may also or vary from ping to ping in cases of interference from
bottom or analysis of bottom layers. Erasedi and Thresholdedi are the number of erased and
thresholded samples between R1i and R2i

Track page

Figure 136. This page contains two tabulated pages. One holds feature options and the

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other held the feature library

Track feature options page

A few of the features that can be selected in the feature library have various options
controlled in the feature option page. As an example, the track feature Mean TS can be
calculated in various ways as described below.

TS features panel
Percentile TS
One of the track features found in the track feature library is the TS percentile. By default
the upper quartile (75% percentile) is presented. This can be altered in this edit box.
Calculate mean TS in the logarithmic domain
If this checkbox is checked, Mean TS will be calculated directly by summing the echoes
TS values and dividing on the number of echoes. The check box will influence on the
calculation of the mean TS of individual fish tracks, on the size distribution generated from
a set of fish tracks in a fish basket and on the result seen in the Oscilloscope window in 2D
mean display mode.

If not checked, Mean values will be calculated in the linear domain.

Correct TS according to aspect checkbox
The track feature Mean TS Adj. (adjusted) located on this dialog's feature library page will
now be aspect corrected according to the setting of the Aspect detection panel.

Aspect detection
This panel is visible only when the Correct TS according to aspect checkbox is checked.
Two options are available;- Obtained from track and fixed angle. If obtained from track is
selected, aspect will be estimated by linear regression through each track. The detected or
the fixed aspect angle will be applied together with the regression data for the selected
species to estimate the Mean TS Adj feature. Thus, it is important to select a regression
containing aspect.

Apect angle panel

Contain options for how the aspect angle feature should be caclulated. Aspect angle is one
of the feature selectable in the Feature Library
Environmental calibration 1 and 2
Method 1enable correction by a simple linear equation while method 2 can apply a series
of different corrections. Method 2 is under construction and not fully tested (29.01.2008)

What is environmental calibration?

Echo sounder calibration should be done vertically in open water with no disturbance. The
environment may influence on the echo sounder. E.g. in horizontal shallow water
application the standard target may look larger than in open vertical water and even
increase with increasing range. One possible reason for this is that the echo sounder
assumes that transmission loss is caused by spherical spreading, while something between
spherical and cylindrical spreading may be more correct. This because the sound may be

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trapped in a waveguide formed by bottom and surface or by thermoclines.

How to do an environmental calibration

Rather than recalibrating, one should measure TS of a known target as a function of range
and let the system adjust TS of tracked targets according to how the environment modifies
the beam at various ranges

1. Use a target that is heavy enough to stay fairly stable in the beam in cases with
water current. If a nonstandard target is applied, measure its actual acoustic size in
open water before or after the environment calibration.
2. Place the target in the center of the beam at various ranges and measure paired TS,
range values.
3. Turn on the Environmental calibration checkbox in the System configuration
dialogs Track feature option page(F9) and fill out the target size and the measured
range and TS value pairs. In the System configuration dialogs track feature library,
turn on the Mean TS Adj. feature. This track feature will now show the corrected
TS value for all tracked targets.

Correction is calculated by linear interpolation and extrapolation based on the measured

Range, TS pairs.

Beam mapping
Place the target at the bottom and in the middle of the beams horizontal centre. Start the
echo sounder recording simultaneously as you start to lift the target from the bottom to the
surface with slow constant speed. Stop recording as soon as the target reaches the surface.
Use the scilloscope (Analysis/Data insight/ Oscilloscope) and study the trace from the
target. This will reveal whether the beam is reliable or not and how the beam fills the water
column.

Track marker panel

Tracking setup with auto color marking allocates different colors in a loop of 8 colors to
mark thraks. This panel let you select colors and pen thickness.

Track feature library page

Figure 137. Track feature library

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See the section: Track feature description later in this chapter for a full description of the
available features and how they are estimated.

This library contains the features calculated from a track. Whenever echoes are combined
into a track, the track features selected in this library will be presented in the feature list
box located in the classification window. The selected features will also be presented for
each track stored in a fish basket. Due to the number of features, it is not convenient to
display all. The library enables the operator to select a few to be displayed at a time.

Track features are important for the classification methods and for generation of track
statistics. The following groups of features are defined

Select buttons:
Check on or off all available features in the list
Export buttons
The first copies all track feature names to clipboard. The second includes the explanations.

Update button
To increase processing speed, only the selected features are calculated. If one have tracked
with one set of features on, and then turn on more features, the targets tracked prior to the
newly selected features will not have the new features estimated, but will show default
values. Update force the system to reestimate all selected features also for the previous
tracked targets. Normally the system will detect if tracks need to be updataed automatically
when the ok button is pressed, but there are a few situations where one may want to do this
manually by pressing the update button.

Species page
The species page holds two tabulated pages, the species selection and calculator page and
the species database page.

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Species selector and calculator page

Figure 138. The System configuration dialog's Selector and calculator page

Species selection
Select species to be applied in the conversion between TS, length and weight for the
biomass analysis and the fish baskets.

1) Type one or more numbers in the Species Id edit box. Multiple Id numbers must be
separated with space or comma.
2) Check that the selected species has appropriate regression coefficients in the grid
below the selector.
3) Verify and edit the probability for each selected species in the bottom grids left
column.

Each Id number is an id to a fish, plankton or other target described in the database located
in the specie database page. The regression data can be edited in the species database page.

Multiple species
When two or more equations are selected and apportioned with a percent of occurrence,
the system convert the TS of an echo into two or more lengths TS-> L1, L2. The average
length is then found as an average weighted by the applied probabilities. See section
Multiple species conversion, later in this chapter.

Calculator
The calculator provides a quick way to test the selected species and to see how the applied
regression data work on given TS or length values.
Length edit box:
Type a length and press update to convert length to weight.

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TS and aspect edit box

Type a TS value and an aspect angle and press update to see the resulting length.

All selected species will be applied in the calculation

Species database page

Figure 139. The System configuration dialog's Species database page

The species database consists of a grid containing regression coefficients. Each row
describes one species, ts coefficients and additional information about the measurements.
Two sets of coefficients are found for each species. The first set enables conversion
between TS and length. The second set enables conversion between length and weight.

Editing the database

 Double click a cell and then type the new data
 Press the insert button to insert a new row
 Press the delete button to delete a selected row.
 The number seen in the Insert and Delete buttons indicate the last double clicked row
and where the action will take place.
 See also the section "Pictures and text files"

Save and load, export and import to and from spreadsheets

The database can be edited directly from Sonar5 or from any spreadsheets capable of
saving the database in plain text with the cells separated by tabulator. To see the file
format, save the database to a file with the save button and open it for example in Excel.
Sonar5 expect to find the database files in the subfolder fish database under the program
folder. As an example:

C:\Balk_Lindem\Program\Fish_database\ Fish_Database.txt

will be loaded automatically when the program starts. If the file does not exist or do not

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contain the correct keyword at the first line, a small default example database will be
loaded.
The keyword is ;FishDataBase and must be printed exactly as here. If not, the program will
give a warning when the file is tempted loaded. This has been done to avoid loading of non
fish database text files which may cause errors during loading and later use.

Pictures and text files

Double click with the mouse in one of the white cells in the base will select the species in
that row. The Id, Species, Latin name and Local name will be presented on the top panel of
the dialog. If a picture and a text description are available this will also be presented.

It is the text in the Species column that link the picture and text file to the species. The files
are supposed to be stored in the same folder as the fish_database or in any subfolders.
Pictures must be in jpg format and text files in .txt format. Text file can be generated by
directly typing or copying the text into the dialogs upper left memo box and then pressing
the save button underneath. Next time that species is selected, the information will be
presented.

Examples:
Species column Text file Picture file
All species AllSpecies.txt AllSpecies.jpg
Atlantic salmon Atlanticsalmon.txt Atlanticsalmon.jpg

Meaning of the columns in the species database

Id-column
This is the key in the database. The id number selects species. When the id number is typed
in the catch basket the species with that id will be presented. The same goes for the
analysis. The Id number is not a row number and may be sorted in different ways.
Species-column
This column describes the species or regression data with a name such as Pike or All
species
The text is presented most places in the program. e.g. as labels in the biomass window. The
text is also used to locate the picture and the text file name. See description later.
Latin and Local columns
Free text for information.
TS-Eq. column
Always apply 1 here. Later more equations may be added. Then this column will select
among the available equations.
Length column
Free text to inform the operator about how the length was measured.
kHz
Free text to inform the operator about the frequency applied in the measurement of the
regression data.
A, B, C, D, k, u1 columns
Coefficients for the TS to length equation.

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Comment
Free text to inform the operator about the TS / Length conversion method.
W/L-Eq. column
Two equations are available for length weight conversion. Select the equation here.
P, Q, R, u2, u3 columns
Coefficients for the selected weight / length equation.
Comment
Free text to inform the operator about weight / length method.

Catch basket page

Figure 140. System configuration dialog's Catch basket page

Fish in the catch basket can be applied

1. to calculate length and weight for tracked fish.

2. to calculate weight in biomass estimation
3. to let biomass estimation present the size distribution in length and weight instead
of TS
4. to scale the biomass result into species and size classes
5. as a source for the size distribution needed by biomass estimation.

Principles
Each line in the catch basket describes the number of fish in one size class for one species.
Multiple species are allowed. The species is identified by an id number. This number must
have been registered in the fish database. Because the same specie may be registered with
different frequencies and aspects in the base, the operator must ensure that it is the correct
ID number that is selected.

Estimating length and weight of tracked fish by Catch basket

When tracks are formed by manual or automatic tracking, length and weight are calculated
automatically. To see the length and weight for a track, length and weight must have been

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selected in the track feature library. See the track feature library section in this chapter.
The calculations are based on species and probabilities selected in the General setting page
and not on the contents of the fish basket directly. (See the general system setting page in
this chapter). However, pressing the apply button will update this setting automatically.

Biomass estimation based on catch data

The content of the catch basket can be applied in biomass estimation as an alternative to
single echo detections. The content in the catch basket will then be applied to establish the
size distribution needed to find the abundance from the echo integration. To do this, a)
convert the catch into tracks by pressing the “Add to fish basket button”. This will result in
a new fish basket in the classify windows fish basket list. The fish basket will be named
“Tracks from catch data”. b) Select the new fish basket in the classify window to tell the
biomass method that this basket is the on to be used as source for the size distribution. c)
Open the biomass windows control dialog and select the method “Catch in fish baskets”
SonarX will now combine sa and sv with the average target strength of each track in the
selected track basket to obtain the abundance. Whether the tracks in the selected track
basket origin from the catch basket or from tracking does not matter to the method. The
setting in the general system setting page (described in this chapter) is used to calculate
the weight. The setting was automatically updated from the catch in the catch basket when
the Add to fish basket button was pressed.

Converting biomass estimation result into weight by Catch basket

When an area in the echogram is analyzed, the biomass window will present the number of
fish and the biomass in weight. The weight is estimated based on the selection in the
General setting page and not on the contents of the fish basket directly. (See the general
system setting page in this chapter). Pressing the apply button will update this setting
automatically.

Scaling the biomass result into species and size proportion by Catch basket
Double clicking in one of cells in the biomass windows result grid will open a dialog
presenting the biomass scaled by catch. (See chapter 8, section Biomass scaled by catch
statistics) This dialog reads the content of the catch basket directly, looks up the regression
parameters for each species in the catch basket and scale the abundance estimate into size
classes and numbers of each species.

Using the Catch basket dialog

Adding new lines to the grid
The upper left panel controls the adding of Catch basket. Select the fish id number to see
the wanted fish name. The id number is the one that identifies the species in the fish
database. When a number is selected, the registered fish for that number will appear. Fish
that are not registered in the base cannot be applied. Set the number of new lines and press
Add will add that number of lines with the selected species to the Catch basket grid. The
length of the fish and the number of occurrence of that fish with the given length are edited
directly in the grid.

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Deleting lines
Write down the start line and the number of lines to be deleted in the delete panel. Press
the delete button to delete the lines. The line to start deletion from can also be set by
clicking at the row in the grid with the mouse.
Apply button
Pressing this button will update the species selection and probabilities in the dialogs
general system setting page.
Add to fish basket button
Pressing this button will generate a fish basket in the classification window and add each
fish in the Catch basket as a track. It will also update the species selection and probabilities
on the general system setting page.
Save button to export Catch basket
Pressing the save button saves the Catch basket to a text file on the working directory. If
the suggested default name Catch_basket.txt is used, this data set will be loaded
automatically next time the program is started. The file can be edited in other spreadsheet
programs like Excel if Excel saves the file in plain text with tabulators as column
separators.
Load button to import Catch basket
Pressing the load button enables loading of a catch basket file. The file must have the
format showed in the section Catch basket file format below.

Edit Catch basket with other spreadsheet programs

Following the format description, any spreadsheet program may be used to edit the Catch
basket table. The program must be able to save the table as plain text (*.txt) with tab
(tabulator character) as separator between each cell. Hint: Press the add button in Sonar5’s
Catch basket editor to generate an example. Press the save button to store it in a file. Then
open this file in your favorite spreadsheet to see the format. Use the format as a template.
Alternatively, copy the table below to clip board and paste it into your sheet.

Catch basket file format

Semi-column ";"in the beginning of a line is regarded as a comment and discarded, except
for the first line where the keyword ;CatchBasket will be checked. Here the first part of the
line must contain “;CatchBasket” written exactly as here to avoid a warning message
when the file is loaded. Each column is separated by a tabulator sign. There are 5 columns
containing the following information

;CatchBasket ; code name to avoid conflicts with other txt files

; Fish count and species composition.
; Each cell is separated with tabulator
; Semi colons are used as comment lines.
; Row no. Species Species Count Measured length (cm)
id
1 1 Herring 2 8.25
2 1 Herring 7 8.75
3 1 Herring 3 9.25
4 1 Herring 1 10.25

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5 1 Herring 1 11.75
6 1 Herring 23 12.25
7 1 Herring 75 12.75
8 1 Herring 82 13.25
Table 8. Catch basket table example.

Col no. Contains Comment

1 Line number Will be renumbered by the system
2 Species ID Index link to an entry in the fish database
3 Species name Text that will be extracted from the fish database
4 Count Number of occurrence of the selected species
5 Length (cm) Length of the selected species
Table 9. Catch basket table column description

Track feature description

See also the Tracks page section earlier in this chapter for information on how to select and
control the features .
Regnr
Track registration number. Each track is given a unique number when it is generated. The
number is applied for reference purpose.
Filename
The filename of the echogram file where the track was found.
Comment
Operator can write a comment about a track.

Track time 1
The time when the track entered the beam. Format hh:mm:ss, h=hour, m=minutes,
s=seconds.

Track time 2
The time when the track entered the beam in seconds from midnight.

Track date
The month and day when the track was detected. Format mm.dd m=month d=day.

Duration
Number of seconds from the track entered to it left the beam.

Size features
Mean (TSc) and Mean (TSu)
The subscript c and u is applied to indicate off-axis compensated TSc or uncompensated
TSu.
Mean TS is the mean value of all echoes in a fish track. By default, MeanTS is calculated

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in the linear domain. The system can, however, calculate mean TS in both linear and
logarithmic domain. The selector is located in the upper left side of the system
configuration dialogs General system page. This dialog can be opened from the Utility
menu. We have included both options because some users wanted the possibility.
Mathematically, however, the linear domain is the correct.

Linear Mean TS

TSc  TSu  GC( xangle , yangle )

1 N 
Eq. 93 MeanTSc  TSc  10  log  10TScii /10 
N 
 i 1 
1 N 
MeanTSu  TSu  10  log 10TSuii /10 
N 
 i 1 

Logarithmic mean TS

TSc  TSu  GC( xangle , yangle )

1 N 
Eq. 94 MeanTSc  TSc  10  log  TSci 
N 
 i 1 
1 N 
MeanTSu  TSu  10  log  TSui 
N 
 i 1 

Percentile TSc
This feature presents the percentile TSc of a track. By default the upper quartile (75%
percentile) is presented. This can be altered on the system configuration dialogs general
page opened by the menu Utilities=>System=>System configuration. The percentile
divides a sorted data material into parts of hundreds. For the sorted data set with numbers
1,2,3,4,5,6,7,8,9 the 25% percentile is 3, the 50% percentile is 5, and the 75% percentile is
7. The 100% percentile is the same as the max value.

A passing salmon in a horizontal, fixed location application may now and then turn the
side aspect to the transducer due to the swimming motion even if the general trajectory is
not perpendicular to the acoustic axis. If so, max TS may be a better estimator than the
mean TS. However, reports and modeling (Lilja et al 2004) indicate that some tracks may
return a few flash echoes that are much stronger than normally expected according to the
fish size. Using e.g. the 90 percent percentile can be a way to avoid overestimation of the
fish size by suppressing the flash echoes.
Max TS
Max TS is simply the TS of the single echo in a track that has the highest value. It is the
same as the percentile TS when the percentile is set to 100%.
CV (TSc)
CV(TSc) is the coefficient of variability among echoes in a track. the feature is calculated
according to the following equations.

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1 N
TS   TSci
N i 1

Eq. 95 std (TS ) 

1 N

N  1 i 1

TS  TSci 
2

 std (TS ) 
cv (TSc)  Abs    100
 TS 

Mean sigma (cm2) and CV sigma (%)

Mean sigma is the mean acoustic cross section area of a tracked target while CV sigma
denotes the coefficient of variability. Mean and CV sigma is calculated from the individual
off-axis compensated TSc values in a track. The following equations estimate mean and cv
sigma.
1 N
  4 10TSci / 10
N i 1

Eq. 96
std ( ) 
1 N
  i
N  1 i 1
 
2

std ( )
cv ( )   100

MeanSigma    10000cm 2

Note that Mean sigma is presented in cm2 (100x100 square meters). The reason to this is
that it improves readability when sigma is printed in tables.
Sigma relates to TSc by TSc  10 log   
 4 

MeanTSadj (dB)
Target strength compensated according to the track aspect and selected species. Aspect is
found by linear regression of the fish tracks single echo positions.
TSq (dB)
TS calculated from tracks detected by image analysis.
Gain Compensation (dB)
Gain comp for a track calculated as Mean TSc- Mean TSu.
Mean TS Image (dB)
TS measured from tracks detected by image analysis.

Fish length (cm)

Mean TSAdj converted to length depending on the selected species. See TS, length and
weight conversion equations in this chapter.

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Fish weight (G)

Mean TSAdj converted to weight depending on the selected species. See TS, length and
weight conversion equations in this chapter.

Track echo-features
Nr. of echoes
Total number of echoes registered in the track
Tot ping count
Total number of ping between the first and the last echo including missing detections.
Max ping gap
The largest number of missing detections in a track.
Sum missing
The total number of missing detections in a track..
Duration (sec)
The time spent by a track in the beam. If the first and last echo in a track is located in
different ping, duration is defined as the time difference between first and last ping. If first
and last echo exist in the same ping, which might happen with manual tracking, then the
time difference is calculated from the range difference and the sound-velocity.

Position features
We separate between estimates relative to the transducer and relative to the platform. It is
stated when a feature is estimated relative to the platform. When relative to the platform,
each involved echo position is transformed from a displaced, rotated, paned and tilted
transducer. For mobile platforms, heave, pitch and roll are corrected for as well. Platform
setup is done in the Utilities=>Parameter=>Application dialog. If all values here are set to
zero, platform coordinates and transducer coordinates will be the same.

Center of gravity (CG) is the mean position of the track. CG describes the track center seen
from the transducer when all echoes are weighed equally. The standard deviation of the
position values describes the distribution of echoes around the CG.

 pos  ath , alo , R 

1 N
Eq. 97  c.g    ath, alo, R  i
N i 1

1 N
 std (c.g )    c.g.    pos  i 2
N  1 i 1

Where N = number of echoes in the track. <pos>= 3D-vector describing the position of an
echo..

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Alo.

Cg
. Ath.

Figure 141. Definition of the cg-vector.

Ath (cg), Alo(cg), R(cg)

Spherical coordinates relative to the transducer. Ath and Alo is measured in degrees while
R is measured in meter. Alo and Ath is short for the alongship and athwarthship angle
while R means range. Cg means that it is the center of gravity for a track that is reported.

Std (Ath c.g.), Std (Alp c.g.), Std (R c.g.)

Standard deviation of the involved echoes in a track around the tracks c.g. point.

Start pos x, Start pos y, Start pos z

Cartesian positions of the first echo in a track relative to the base platform.
These features are mostly used by people working with horizontal fixed location
applications wanting to know where in the river a track starts. x is then up/down stream. y
is the depth in the river and z is the distance out in the river relative to the base platform. If
the base platform is located on the riverbank and you move the transducer platform around
in the river, you will still see the correct place in the river where the targets have been
detected.
Exact range Xe, Ye, Ze
These features are not selected in the feature library, but presented when individual echo
positions from a track are exported or presented in the track information dialog. x, y, z
referee to Cartesian coordinates with x in the along ship, y in the athwart ship and z away
from the transducer. The e for exact indicate that the features are calculated relative to the
base platform. We use subscript e for exact and not b for base platform because this was
made before the base platform was introduced in the system. It will be changed in the
future.

Target depth
Distance in meter from the surface to the targets c.g. independent of whether it is a
horizontal or vertical application.
Distance to bottom
For vertical application, this is the distance between the tracked target and the detected
bottom line. For horizontal application it’s the distance between the target and the
horizontal river bottom profile.

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GPS position
GPS N/S and GPS E/W indicate the position of the echosounder when the track was
obtained.
Target position
Target position is calculated as an offset to the GPS position. Parameters in the application
dialog opened by the Utilities=>parameters=>Application menu are used to find the exact
echo position. Transducer position in the boat and its tilt, pan and rotation are used to find
the target position relative to the boat. Roll, pitch and heave are applied to find the target
position relative to transect. Ship heading is found from the GPS signal.

Track distance-features
This group of features describes the distance traveled by a track relative to the selected
Cartesian coordinate system. If all parameters in the application dialog are set to zero, the
base platform will be the same as the transducer. For a fixed application with parameters
set different from zero, base platform can be moved to a fixed point on shore. For a mobile
survey base platform will be a defined point on the boats roll and pitch axis.

Distance between the first and last echo in a track

DistFirstLast X, DistFirstLast Y and DistFirstLast Z in meters denote the distance between
the first and last echo in a track along the platform related axis.
Sum Ath dist (deg) , Sum Alo dist (deg)
Sum ping to ping traveled dist. in Ath and Alo direction

Direction step counter

Mean Steps Ath, and Mean Steps Alo
These features tell whether the main movement was in positive or negative direction. The
features sum the number of movements in positive direction and subtract the number of
movements in negative direction. The result is divided by the total number of movements.
A track with N echoes will have N-1 movements. Zero movements are not counted. The
DC features varies between +/-1

1 N 1   1 | xi 1  xi |
MeanSteps X  
N  1 i 1   1 | xi 1  xi |

Where x can be ath or alo, and N is the number of echoes in the track
Sum echo dist. (m)
This is the sum of the Euclidean distances between all platform-related echo-positions in a
track.

N 1
SumEchoDist   xi1  xi 2   yi1  yi 2  zi 1  zi 2
i 1

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MeanEchoDist. (m)
Sum of Euclidean distances between all platform-related echoes in a track, divided by the
number of echoes-1 in that track.
SumEchoDist
MeanEchoDi st 
N 1

Velocity-features

Time and velocity between neighbor echoes are estimated according to the following
equations
Ping i 1  Ping i
t 
PingPerSec
Eq. 98
Pos i 1  Pos i
Vi 
t

Speed first last (m/s)

Speed calculated between the first and last echo along the platform coordinates.
SpeedFirst Last  VxFirstLas t 2  VyFirstLas t 2  VzFirstLast 2
Mean (echo speed) (m/s)
Mean speed between all platform related echo positions. The speed between neighbor
echoes are summed and divided by the number of summed speeds.
1 M
Mean(V )   V     Vi 
M i 1

Vx first-last, Vy first-last, Vz first-last

Velocity in (m/s) between the first and last echo along the platforms x, y-axis and z-axis
 DistFirstL ast 
 V FirstLast 
Duration
Mean velocity (Vx) , Mean(Vy). Mean(Vz)
Mean velocity in m/s between all echoes in a track along the platforms x, y and z-axis.

Std(Vx) Std(Vy), Std(Vz)

Standard deviation in a tracks velocity in the platform related x, y and the z-domain

std (V ) 
1 M
 
M  1 i 1
 V   Vi 2

Absolute velocity
AbsVx , AbsVy and AbsVz are the sum of absolute distances between all platform related
echoes in a track divided by the track’s duration. Three features are estimated, one for each
platform coordinate axis. When AbsVx is estimated, only the x-components of the echo
velocities are applied and so on.

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1 M
AbsSpeed | V |  | Vi |
M i 1

Ship-velocity (m/s)
Two features, Ship-vel S->N and Ship-vel W->E are estimated. They contain the ship
velocity when the track was detected

Track behavior-features
Change direction
Change dir. Alo., Change dir. Ath, Change dir. R calculate the average number of times a
track changes direction.
Assume that a track moves three steps to the left and one step to the right, then Change dir.
=1

Net sum steps

“Net sum steps Ath” and “Net sum steps Alo” count the signed steps along the Alo and
Ath axis. A track with 4 echoes can move three steps. If two steps are forward and one step
is backward, then the Net sum steps = 1.
Crossing axis
Crossing Alo axis and Crossing Ath axis counts the number of times a track is crossing
the axis.

Smoothness 1
Smoothness of a track is defined as the distance between the first and last echo divided by
the sum of distances between all echoes. A totally straight or smooth track will have an
Sm1=1. Sm1 will decrease when smoothness decrease.

x1  x N 2   y1  y N 2  z1  z N 2
Eq. 99 Sm1  N 1

 x
1
i 1  xi    yi 1  yi   zi 1  zi 
2 2 2

Where x, y and z are the Cartesian positions relative to the transducer and N is the number
of echoes in the track.

Sm1 is likely to decrease with increasing number of echoes in a track. This effect may be
compensated for by dividing with a number related to the number of echoes in the track.
We have experienced good results by dividing with 10log(N+10), returning 1 for N=1 and
slowly increasing with N. This is not included in the estimation of sm1 but the operator
may apply it on exported results.

Smoothness 2 (sm2)
Smoothness 2 is based on the mean cosine between three and tree echoes throughout a
track. First the angle θ1 between echo 1, 2 and 3 is calculated. Then the angle θ2 between
echo 2, 3 and 4 is calculated and so on. With N being the number of echoes in a track, N-2
angles can be found. As an example, assume a track of three echoes (N=3) Then if the

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track is straight, all echoes lies on a line and the angle between echo 2 and the two others
will be 180 deg and sm2 will be zero. If there are a 90 degree angle between the tree
echoes sm2 will output 0.5, and if the track return back to the start the angle will be 0 deg
with sm2=1 indicating a total non smooth track.

Output: The formula has been arranged so that sm2 for a total smooth track with 180 deg
angle between all echoes will output 1 while a track that makes a 180 deg bend between
three echoes will output 0. A track of four echoes where three is in line and the last echo
makes a 180 deg bend will output a value of 0.5

Figure 142. Sm2 for a track as a function of angles between neighbor echoes

1 N 2 1  cos( i )
Eq. 100 Sm2  1  2
N  2 i 1

Y.

.

X.

Figure 143. Definition of the ith angle  used to calculate smoothness 2.

Smoothness 3 (sm3)
R-squared or value of the tracks alo, ath angle positions. The R-squared value is the square
of the Pearson product moment correlation coefficient. Sm3 will take on values in the span
[1..0> where 1 indicate a perfectly smooth track.

2
 
Sm3  
 ( x  x)( y  y ) 
2 

  ( x  x)  ( y  y ) 
2

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XY-Angle (deg)
This angle indicates the angle between the x axis and the y axis. It is presented in degree
and estimated by linear regression. All x and y positions are applied to find the line
regression line y=ax+b. Arc-Tangents to the inclination a is returned as the xy-angle.
XYangle=ArcTan(a). The unit is degree.

XY-domain
Y

Regression
line Y=cx+d

=xy_angle =ArcTan(c)

Figure 144. Definition of the xy-angle. X is defined to point in the athwart ship direction
while y is following the alongship direction
Aspect angle (deg)
Aspect angle is the tracks angle or fish tilt towards the echo sounder. 90-deg indicates that
the echo sounder sees the fish in the side or dorsal aspect. The aspect angle can be
calculated with two different methods and with three options for the axis. This is controlled
on the Utilities => System configuration dialogs => Track => Feature options page. Here
one can select between the linear regression and the average method. The three options for
the two methods are xy-z, x, z, and y-z. Normally one want to use the xy-z option giving
the overall aspect, but in some situations one want to find the aspect relative to only the x
or the y-axis.

Tracks with 1 echo:

Tracks containing only 1 echo will always be reported with an aspect of 90 deg.

Aspect by linear regression

Linear regression returns the inclination (a) and the offset (b) that estimate the best fitted
straight line through the fish track for the straight line y=ax+b. The reported aspect angle is
fond from the inclination (a) in the following way

Aspect  Degrees(arctan(a))  90

Aspect by average

First the distance between two and two neighbor echoes are calculated.

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dxi  xi 1  xi
dyi  yi 1  yi
dzi  zi 1  zi

where x, y and z are the Cartesian coordinates. Then the ith angle is found according to the
method a, b or c selected in the System configuration dialogs “Track settings” page.

 
 dzi 
Method a ) anglei  arctan  
 dx 2  dy 2
 i i 
 dz 
Method b) anglei  arctan  i 
 dxi 
 dz 
Method c ) anglei  arctan  i 
 dyi 

These angles are flipped to obtain angles relative to the acoustic axis in the following way

 anglei  90 : denom  0

anglei  
anglei  90 : denom  0

Where denom is the denominator in the arctan equations above depending on the selected
method. When all angles have been found for a track, the average angle is output as the
track aspect angle.

1 N 1
aspec angle   anglei
N  1 i 1

As an example, select method (b) and assume a track of two echoes with (x, z) co-ordinates
equal to (1, 15.1) and (2, 15.2). Then we have
dx  x2  x1  2  1  1
dz  z2  z1  15.1  15.2  0.1
angle  arctan(1 /  0.1)  5.7

Since dx>0 we add 90 deg to obtain the final aspect angle of -5.7 + 90=84.3 deg aspect
relative to the acoustic axis.

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transducer
x

Aspect angle

Acoustic axis

Figure 145. Definition of the aspect angle.

Track quality
Track quality includes features that tell something about the quality of detected tracks. This
must not be confused with echo quality witch tell something about the quality of individual
single echoes.
Detection probability (DP)
No. of echoes / no. of pings. The number of single echo detections divided by the number
of pings between the first and the last detected echo in a track.
Track quality (TQ)
No. of echoes / (Sum missing +1). The number of single echo detections divided by the
number of missing detections +1.
Std(Missing)
The spreading in missing echoes throughout the track. (Experimental feature)
Average echo length (cm)
Echo length (EL) is the duration of an echo, measured at a certain level below the echo’s
peak intensity. EL is calculated at -6,-12 and -18 dB below the peek for each single echo in
a track. The averages for all echoes are presented. Note that this feature demands that an
Amp echogram are available and that the range resolution of the Amp echogram will
influence on the result. This because EL is found by looking up the original echoes in the
Amp echogram. Since this is a relative computer demanding task, it is only carried out
when this feature is selected in the feature library. If selected in the library, it will be
presented in the classification window and in the fish basket, but not in the track
information dialog.

Image tracking-features
The following features are only available when tracks have been detected with image
analysis.

Q-Width height rat. -

The detected regions ping / sample ratio

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Q-PingRangeArea
Area of the detected region measured from the number of samples in the detected region.
Q perimeter #
Q perimeter is measured as number of samples along a tracks rim or perimeter.

Features obtained by combining the SED and the Amp echogram

The following features have been developed together with Robert Kieser at Fisheries and
Oceans Canada. The section is partly written by R.B. The aim has been to test new features
suited to classify targets. The features differ from other track features in the way that they
cannot be calculated purely from the tracked single echo detections. Instead, the positions
of the detections are looked up in the Amp echogram. The samples surrounding each
detection are applied. An average is presented for each track.
Mean echo length
Echo length or pulse width is shown at relative echo levels (REL) of -6, -12 and -18 dB.
The length is presented relative to length of the transmitted pulse. The output value for
each track is an average of the echo length measured for each individual echo in the track.
Linear interpolation of the amplitude data is used to define echo length more accurately.
Interpolation is necessary to obtain a reasonable estimate. The linear interpolation is given
by

r  ri  i
Eq. 101 
ri 1  ri  i 1   i

where y i are the sample values in units of amplitude (eg. for TS sample data
TS
  4  10 20 ) and xi are range or time. Indices i and i+1 point to a sample value to the
left and right of the width start point. And x and y are rang and echo level at that point.
Calculations for the width end point are analogous. Interpolation is not required for any of
the following features.
Mean echo integral (Ei) mW )
The echo integral is shown at relative echo levels (REL) of -6, -12 and -18 dB. The unit is
mW. The output value for each track is an average of the echo length measured for each
individual echo in the track. The echo integration value Ei is given by:

Eq. 102 Ei    i 2
i
Center of gravity, STD, Skewness and Kurtosis
The following features are shown at relative echo levels (REL) of -6, -12 and -18 dB. The
features are calculated for each echo in the track and the mean value is presented. The
features are calculated by interpreting the samples in the single echo pulse as a histogram
with the range of each sample ri as the measured quantity and the amplitude σ of each
sample as the frequency of the distribution. We have:

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Figure 146. Echo pulse with 5 samples at increasing range

m
sum  s    i
i 1
m
Eq. 103 C p    i ri p
i 1

1
Center of gravity  C1
s
1/ 2
 1  1 2 
Std    C 2  C1 
 s 1 s 

1  2 3
Skew   s  C3  3C1C 2  C1 
s  1s  2Std 3  s 

s 1  6 3 4
Kurt   sC4  4C1C3  C12 C 2  C 
2 1 
s  1s  2s  3Std  4 s s 

3
s  12
s  2s  3

where summation is over the m sample points that are in the peak window. See (Sokal and
Rohlf, 1981) page 114.
Foreground Sv
Foreground Sv is shown at relative echo levels (REL) of -6, -12 and -18 dB. The feature is
calculated for each echo in the track and the mean value is presented. The sv value for each
sample within the -6dB, -12dB and -18dB pulse is summed for each detection in a track
and divided on the number of samples. The output describes the volume reverberation of
the tracked target.
Background Sv
Background Sv is estimated from relative echo levels (REL) of -6, -12 and -18 dB. The
feature is calculated for each echo in the track and the mean value is presented. The sv
sample values found before and after the pulse defined by the -6dB, -12dB and -18dB are
summed for each detection in a track and divided on the number of summed samples. The
output describes the volume reverberation surrounding the track at the three levels.

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Mean area
Track length multiplied with the mean echo length.
Length height ratio
The ratio between the track lengths measured in number of detections divided by the mean
echo length described above.
Phase dev
Standard deviation of sample angles are estimated from the samples involved in each
individual echo in a track. The standard deviations are summed and divided by the number
of echoes to form the mean standard deviation. The results are presented as PhaseDev(ath)
and PhaseDev(alo).

TS, length and weight conversion

TS length conversion
Two equations are available for selection in the length to weight panel located in the
Species database page. See described in this chapter.

Eq 1 : TS  A  log( u1  Length )  B  C  cos k (2  a)

Eq 2 : TS   A  log( u1  Length )  B   C  log( u1  Length )  D cos k (2a)
 C  log( u1  Length )  D 

The first equation can be applied in vertical and horizontal applications. Setting C=0
restores Loves formula. The second part has been published by Lila et al. (2000). Here a is
the aspect angle obtained from the fish tracks. u1 is a scaling factor. Sonar5 expect the
length to be measured in cm. If the regression coefficients were developed to produce
length in mm U1 must be set to 10 and so on.

The second equation has been developed by Duncan and Kubecka, (1995). It is more
complicated than Lilja's, but reflects that side and tail aspect follows non parallel
regression lines. This gives an increased accuracy in the conversion and de convolution.

The inverse function gives the length when TS is known:

TS  B C cos k ( 2a )
1
Eq 1 : Length  10 A
u1
TS  D  ( D  B )cos k ( 2 )
1
10 C  ( AC )cos ( 2 )
k
Eq 2 : Length 
u1

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Length to weigh
1 : Weight  u 2  P  (u3  Length) Q
2 : Weight  u 2  e P  Q ln(u3  Length  R )

Whether eq. 1 or 2 are used is defined by the number in the W/L-Eq. column Again u are
scaling factors applied to ensure that length are given in cm and weight in gram.

And the inverse functions are ....

 weight 
log 
 Pu2  log(u )
3
1 : L  10 Q

 Weight 
ln   P
 u2 
1
2: L  e Q

u3

Multiple species conversion

We can develop regression coefficient for multiple species and apply in the conversion.
Otherwise we can apply regression coefficients developed for individual species. The
principle is that we run each of the selected species through the conversion formula before
finding the mean value from the results.

Multiple species TS to length

Assume two species e.g. pike and bream with 10% and 90% abundance composition
respectively. The same TS will scale to different length. The conversion is done as follows:

TS ccosd ( 2 a )
1
LengthBream  10 A
(Bream coef.)
u1
TS ccosd ( 2 a )
1
LengthPike  10 A
(Pike coef.)
u1
Length  0.9  LengthBream  0.1 LengthPike

Multi species length to weight

Weight Brim  u 2  P  (u3  Length ) Q

Weight Pike  u 2  P  (u3  Length ) Q
Weight  0.1Weight Bream  0.9 Weight Pike

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12 Tracking

Main menu , Tutorials

WHAT IS TRACKING ......................................................................................................................................... 294

SET UP THE SYSTEM FOR TRACKING ................................................................................................................. 294
TRACKING METHODS ....................................................................................................................................... 294
Click tracking ............................................................................................................................................. 295
Manual tracking ......................................................................................................................................... 295
Automatic Multiple Target Tracking (MTT) .............................................................................................. 296
CFT Cross filter tracking ........................................................................................................................... 304
TRACKER POPUP MENU .................................................................................................................................... 305
STORING AND DELETING TRACKS..................................................................................................................... 305
ADDING AND REMOVING ECHOES IN A TRACK.................................................................................................. 307
DISPLAY STORED TRACKS ................................................................................................................................ 307
Alternative 1 Goto first, prev, next and last ............................................................................................... 262
Alternative 2 Select track in the fish basket ............................................................................................... 262
Alternative 3 Replay the content of a fish basket ....................................................................................... 262
RESTRICTING TRACKING TO LAYERS................................................................................................................ 262
I NEED HELP TO GET THE TRACKER TO TRACK CORRECT .................................................................................. 263
TRACKING PERFORMANCE DIALOG .................................................................................................................. 263
AUTOMATIC PARAMETER DETECTOR ............................................................................................................... 264
Preparation ................................................................................................................................................ 265
Detecting parameters for the Track supporter ........................................................................................... 266
Detecting parameters for the gates and predictors .................................................................................... 267
Detecting weights for the association ........................................................................................................ 267
CROSSFILTER TRACKING .................................................................................................................................. 267
DEMONSTRATING THE EFFECT OF VARIOUS ALPHA BETA PARAMETER SETTINGS ............................................. 268

Background material is found in Balk and Lindem, (2001 a) and in (Blackman, 1986)

Balk and Lindem 293

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What is tracking
Tracking is the process of combining successive echoes from different targets into separate
tracks. Echoes to be tracked can be single echo detections seen in the SED echogram or
clusters of samples with intensity above the background reverberation level seen in the
Amp echogram. Tracking can be a manual process where the operator either tells the
system witch echoes to connect or an automatic process. With manual tracking, the
operator selects the echoes to be combined with the aid of the mouse. With automatic
tracking, a computer algorithm determines the combinations.

When a set of echoes has been combined, these echoes form a track. Whenever a track is
formed, it can be plotted in the position diagram window and marked in the echogram
window. Track features, such as mean target strength and velocity, can be calculated from
the individual echo positions in the track. The track and the calculated features can be
studied graphically or numerically in the position diagram and in the Track feature dialog.
(See chapter 9).

Set up the system for tracking

To set up the system, use one of the setup templates found in the main Analysis menus.
The menu setup opens a dialog with and templates and setup modifications to chose. The
menu Analysis=>Analysis=>Setup=>Tracking provides a list of pre-made templates.

Figure 147. Select a tracking setup template.

Tracking methods
The upper panel contains the method selector. The selector has the following options

 CFT = Crossfilter tracker (Automatic)

 MTT = Multiple target tracker (Automatic)
 Manual = Operator combines echoes manually by hand
 Click = Click counting
 Off = No tracking

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Click tracking

Figure 148. Tracker windows method selector when click tracking is selected
Items in the method panel
? button gives quick help for the method panel.
dbl. checkbox indicate that a click must be double to register a track.
Options button opens a menu with tools related specially to the selected tracking method.

When click tracking is selected, clicking or dbl clicking in the echogram or multi beam
viewer will generate a track consisting of one echo. The echo has intensity range and time
according to what was found at the mouse tip. See storing of tracks on how to store this
track.

Manual tracking

Figure 149. Tracker windows method selector when manual tracking is selected
Items in the method panel
 ? button gives quick help for the method panel.
 One echo only checkbox will generate individual tracks for each selected echo. See
below.
 Free hand checkbox switch between rectangle or free hand selection of echoes to be
combined by the operator.
 Options button opens a menu with tools related specially to the selected tracking
method.

Manual tracking let the operator combine Single Echo Detections (SED) into tracks
manually with the mouse. To enable fast and smooth tracking different methods are
available. One can draw a rectangle or a free hand line around the echoes to be combined.
When there are high densities of echoes it may be a help to zoom the echogram in on the
region. It may also help to track a target in more than one operation.

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See also the sections

 Adding and removing echoes in a track
 Storing and deleting tracks
in this chapter

One echo only

When one echo in each is checked, each of the selected single echoes will be handled as a
separate track. This can be a useful tracking option.
a) On can see the movement of a fish in the position diagram. The speed can be
slowed down with the tracking speed scrollbar in the upper right corner of the
classification window.
b) Classification tools designed to classify tracks can be applied to classify single
echoes. Features as echo length, TS, position, kurtosis, energy, center of gravity
etc. can be applied in the classification.
c) Fish baskets can be used to store, display and export single echo statistics.

How to do manual tracking example

 Set up the system for manual tracking in the main analysis menu
 Check off the freehand checkbox.
 Draw a rectangle around one or a few echoes from a target in the echogram.
 Press the P-key
 Press the left mouse button down while pointing at all echoes to add.
 Press the space key to store the track.

Automatic Multiple Target Tracking (MTT)

See also the tutorial: 03_Multiple target tracking.ppt in the Help_Tutorial folder

Figure 150. Tracker window when MTT tracking is selected

MTT is short for Multiple Target Tracking. This automatic tracking method was originally

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developed for missile tracking by radars. (Blackman, 1986)

An MTT consists of four main elements. Track supporter, Gating Association and
Prediction. Prediction method can be zero velocity, weighted mean, Linear regression and
Alpha Beta, When Alpa Beta is selected we have an alpha beta tracker. The parameters for
each of these elements are located on separate panels in the tracker window. A simple
parameter panel is displayed by default. Selecting the advanced parameter page will switch
the tracker into an advanced MTT and show the advanced tracking parameters.
Items in the method panel
 ? button gives quick help for the method panel.
 Start button. This button will start the MTT automatic tracking process for the
selected region. When pressed the text turn to Stop which will halt the process as
soon as possible when pressed.
 Free hand checkbox switch between rectangle or free hand selection of echoes to be
combined by the MTT.
 Options button opens a menu with tools related specially to the selected tracking
method.

How to do MTT tracking? An example1:-

 Set up the system for automatic or MTT tracking in the main analysis menu
 Check on the Store track in the classification windows upper left part.
 Press the Start button or
 alternatively draw a rectangle or a free hand line in the echogram around one or a
few tracks.

Simple automatic tracking parameter page

Figure 151. Simple tracking parmeter with constant track support and gating in one
dimension. The advance tracking parameter panel can be "brutal" to a novice user and a
simple tracker panel has been implemented as default.
Max Ping gap
The Max Ping gap parameter tells the system when it is time to regard a track as cold
(passed the beam). If ping gap is tuned as demonstrated in Figure 151, two echoes can be
missing before the track is defined as cold.
Min. Track length
Cold tracks are compared with the min. track length parameter. If the track is too short, it
will be deleted as noise. If not, it will be sent to the classification unit and eventually

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stored. It will also be presented in the position diagram windows and marked in the
echogram.
Track length is measured in number of detections, independent of missing echoes or
movement in the angular domain. In the advanced methods, other options are available.
Gating
The SED-tracker always predicts the position of subsequent echoes in a track under
formation. The gate is placed with the center at the predicted position. If no echo is found
within the gate, a missing detection is noted. If one echo is found, the echo is added to the
track. If more than one echo is found, the echo closest to the predicted position is added.
A small gate may result in tracks being broken up in short fragments. A large gate may
result in echoes from different tracks being combined into one track.
Gate range
defines the gate size in the range domain. The simple tracker does not apply gates in any
other domain. To do so, press the advanced button.

Advanced automatic MTT tracking parameter page

Select the advanced page to see these parameters

Figure 152. Tracker window's advanced tracker page

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Advanced track support

Figure 153. Track support panel with stepwise TL and Ping Gap functions
The track supporter handles new track seeds. It determines when a track getting cold (has
passed the beam) and, whether a cold track should be deleted as noise or accepted for
further evaluation. Ping gap is applied to test the tracks "temperature" and track length is
applied to determine whether a track should be regarded as noise or not. Accepted tracks
can be classified, stored, and presented to the operator in the echogram, position diagram,
fish baskets, and track information window.
Track length (TL) and Ping gap (PG) functions
Track length and Ping gap depends on range. At short range, track length increases with
increasing range due to the shape of the beam. However, the signal to noise ratio is reduced
with range due to increased transmission loss. This results in an increased number of
missing detections at longer ranges. Hence, there will be a maximum point in the track
length function at a certain range. After this range the function will decline. The ping gap
function will increase in a non-linear way. The situation is further complicated by the
influence from the targets. Fish from different species and size groups may be layered or
unevenly distributed. This results in stepwise track length and ping gate functions.
Setting up the stepwise MinTL MaxPG function
Write the numbers directly in the grid. For example the series 10, 20, 30, 40, 0 in the first
line. This will divide the range into one layer from 0..10 m, 10..20 m, 20..30 m and 30..40
m. The zero is a message to the system that 30..40 m is the last layer. Then specify MTL
and MPG for each range bin. The automatic parameter detector can measure TL and PG in
training sets and set up the table. Define the range bins, track some tracks manually, store
the tracks in a fish basket and press the auto param. detect button will do. The system will
detect the TL and PG that will accept these tracks. More over it will detect the best way to
measure the track length. If many range bins have been defined, sufficient number of
tracks must be tracked for each bin.

Measuring track length

Figure 154. Three diffeernt track length measure

Three different ways to measure track length can be selected in the Track supporter. Track
length can be measured in number of detected echoes, in number of pings from the first to
the last echo in the track including missing echoes and in traveled distance between the
first and last echo in deg. calculated in the angular domain. The last measure is less range
dependent than the others, but it is not totally freed due to range dependency in the signal
to noise ratio.

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The TL values in the TL table will differ depending on the way it is measured. The system
stores the defined set of TL value. As an example, Assume that TL has been measured in
Nr of echoes and that the TL values 2, 4, 5 and 7 has been noted in the table for four
different range bins. Selecting angular distance in the panel in Figure 154 may present the
values 4, 4, 4, 3.5 (deg). Reselecting the Nr.of echoes will restore the old setting 2,4,5 and
7.
The Auto param. detector fills out the TL table for all possible TL measure and presents
the selection that gave the best fit according to the tracks in the training set.
Advanced gating

Figure 155. The advanced gating panel

The SED-tracker always predicts the position of the next echo in a track under formation.
The gate is placed with the center at the predicted position. If no echo is found within the
gate, a missing detection is noted. If one echo is found, the echo is added to the track.

Ping gate
Ping gate defines the gate size in the ping domain. The future is well known in post
processing. Hence we can test echoes that will occur well into the future. It might happen
that an echo found two or more pings into the future is better suited than the closest echo
found in the next ping. As an example the echo in the next ping may be a noise-based echo
with a TS very different from the TS in the already combined echoes. If the next echo in
time has a TS value similar to the rest of the track, this might be a better echo to combine
even if a missing detection will occur. Applying high values on association in time and TS
may cause the tracker to skip the nearest echo in time in favor of the next echo.
1 2 3 4 5 6 7 Ping
Gate

e Observations
Estimates

Range
Figure 156. Gating and echo-association including the time domain may result in rejection
of the echo (marked e) when a better-suited echo is located at a later time. This can result
in a smoother or more correct track, but at the cost of an increased number of missing
detections.
Range, Alo and Ath initial gate size
Defines a gate in space measured in meter in the range domain and angles in the angular
domain. Normally the accuracy is higher in the range domain than in the angular domain.
Hence, the gate should be better tuned in range than in the angular domains. Small gates
are applied to avoid combining nearby tracks. At the same time small gates increases the

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chance of splitting tracks into small fractions.

Range, Alo and Ath gate increase with missing ping

If a ping is missing, the chance of finding the next echo within the same gate is reduced
due to noise. The increase gate size parameters let the gate increase with the defined
factors for each missing echo. Too large factors here may result in mixed tracks from
different ranges.

Association and association conflicts

Figure 157. The association unit solves tracking conflicts.

Conflict 1. One track has to choose among several echoes.
If more than one echo is found within a gate, the association unit evaluates each echo. The
best-suited echo, according to the predicted position, is added to the track. Echoes not
found suited are added to the track supporter as new track seeds.

New echos

?
Transducer 

Track
Figure 158. A situation with three echoes in the neighborhood of a track. The tracking
algorithm has to select one of the three, but whitch?
Conflict 2. Many tracks competes for one or a few echoes
Two or more tracks may claim the right to the same echo or echoes. The association-unit
tests all claiming tracks against all new echo candidates. Each echo is assigned a score for
each track and the track -echo combination with the highest score gets the echo. Remaining
tracks have to compete for the remaining echoes. Leftover echoes are given to the track
supporter as new track seeds.

Gap

Result a Result b Result c Result d

Figure 159. Two tracks under formation competing for one and the same echo. Four out of
many possible associations.
The operator can tune the association by adding different weights to the different domains.

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When the predictor predicts the next position of an echo, it also predicts the next echoes
assumed echo intensity or TS. When the association algorithm evaluates echoes, the
Euclidean distances between the predicted echo and the echoes observed within the gates
of all tracks under formation are calculated. Each domain in this multi-dimensional space
is weighted with the user-defined weights, and the result forms the distances between the
observations and the predictions. Shortest distance is the best. Thus a higher weight in a
domain will increase the importance of that domain. As an example, add the value 10 to
the range and 1 to the others, then distance in range will be 10 times more important than
the other domains.
Note that range is measured more accurate than angles and should therefore, in most
situations have higher weight than the angles.
d 2  wr (r p  ro ) 2  w Alo ( Alo p  Aloo ) 2
Eq. 104  w Ath ( Ath p  Atho ) 2  wt (t p  t o ) 2
 wTS (TS p  TS o ) 2
In Eq. 104, w is a weighting factor, r is the range, Alo and Ath the angular positions, t the
time and TS the target strength. Subscript p, o indicates predicted and observed values
respectively.
Prediction

Figure 160. The predictor panel with four predictors and their parameters.
The predictor determines the most probable position for the next echo. The gate is centered
at this position. Prediction is an important element in advanced tracers. Four different
predictors can be selected.
Zero velocity means that the gate for the next echo will be placed in the same position as
the present echo in the track under formation. This is a very simple prediction, However,
with sonar data this predictor frequently turns out to be the best. Tests are presented in
Balk and Lindem, (2001 a)
Weighted mean studies the movement of each echo in the track under formation and
calculates a weighted mean value for the movement. The weights are increased towards the
end of the track. Thus, trends in the near past will weight more than trends observed earlier
in the track. The parameter N controls how many echoes that should be applied at most,
counted from the last detected echo.
Linear regression estimates the next position by applying a straight best fit line through
the last N echoes in the track.
The alpha beta predictor estimates the smoothed position xS from the measured
observation z(k) and the predicted position xP by the application of a constant Alpha and
Beta filter gain.
Smoothed velocity estimates are calculated from the position measurements and the
predicted positions. The elements of the Alpha-Beta predictor are seen in Figure 161. Eq.
105 demonstrates the predictor's estimate and prediction functions.

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x s (k )  x p (k )   [ z (k )  x p (k ) ]

Eq. 105 v s (k )  v s (k  1)  [ z (k )  x p (k ) ]
qT
x p (k  1)  x s (k )  T v s (k )

Here, xS and vS are the smoothed estimates of the observed target cinematic and xP the
predicted position.

, 
Noise Observation
Target z(k)
x xS (k) Predictor
dynamics + Estimator
Vs(k)

xP(k+1 | k)

Figure 161. Elements of the Alpha-Beta predictor.

The effect of tuning the alpha and beta parameters.
A,B Tracking result
0,0 All predicted position will have the same position as first echo in the track
1,0 Same as zero velocity each prediction will take on the same position as the
last echo added to the track.
0,1 The prediction will oscillate with increased amplitude for each movement
between the observed echo positions.
0.5, 1 The predictions oscillates in a damped manner when the actual echoes
moves.
0.3,0.1 Combination of damping and movement amplification that may work quite
well
A graphical test of the commented parameter values is found in the section: Demonstrating
the effect in the end of this chapter.

Special

Figure 162. Special tracking options.

Max. nr. of echoes in a track.
Track supporters commonly deal with min track length. Sonar5's advanced track supporter
also deals with max track length. Echoes from stationary targets produce long tracks.
Hence, tracks from stationary targets can be avoided by limiting the track length in the
same way as the Min. Track length parameter reduces noise-based tracks by removing
short tracks. By default this parameter is set to 1000 echo detections per track.

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CFT Cross filter tracking

Figure 163. Automatic cross filter tracking

The Crossfilter tracer uses image analysis to detect and track target.. While a track consist
of a set of single echo detections, a trace consist of a cluster of samples or pixels. In the
same way as the operator does with manual free hand tracking, the CFT “draws” a free
hand line around each trace. (except that the line is not be seen in the echogram) . Single
echo detections encircled by the line are combined into tracks and stored.

The Setup button opens the CFT dialog where one can tune, test and run the method. One
can also run the method by pressing the start button as with the Auto tracking. See the
section Cross filter tracking in the manual chapter 19 Cross filter detector for more about
this method.

While the Crossfilter is processing, current image analysis command will be displayed in
the bottom of the tracker. To see the complete process, click the trackers tabulated Image
page.

Do not confuse Crossfilter tracking with Single echo detection (SED) based on cross
filtering. Both use the Crossfilter detector to detect traces. The aim of the CFD is to
generate a new SED echogram while the CFT goes a step further by both detecting new
SED’s and combining them into tracks which can be stored in the fish baskets. (CFT can
also be set up to use existing SED)

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Tracker popup menu

Figure 164. The Tracker's menu is a popup menu. Pressing the right mouse button in the
tracker window opens the menu.
Help
opens this chapter if the folder help_doc is available in the program folder.
Auto parameter detection
starts the automatic parameter detector. This is described in the section: Automatic
parameter detection.
Load parameter
loads previous stored tracking parameters from file.
Save parameter
saves the current parameter setting to a file. Note that the setting will be saved in the
systems configuration file when Sonar5 is closed. This setting will be loaded next time the
program starts. Hence, the save menu is only needed when one want to be able to go back
to special setting later. If a particular survey has to be tracked with other parameters than
normally applied the parameter file can be saved in this survey's folder.
Copy parameter to clip board
copies a description of the tracking parameters in plain in text. Use this option for
documentation.
Templates
access the image analysis templates.
Command writer
Opens the command writer tools. This tool help writing image analysis commands for the
command editor in the trackers image page. See chapter 15 Image analysis.
Empty fish baskets before each analysis
Check this menu item on to empty fish baskets before each new tracking session is started.

Storing and deleting tracks

Tracks are stored in fish baskets located in the classify windows basket list box. If the
classify window is not seen on the screen, a fish basket panel containing one basket for
track storing will appear in the tracker window. In addition, tracks can be stored as text

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lines in the mouse tip monitor opened by the echogram menu.

Figure 165. Classify windows basket list box with three baskets.

Figure 166. Tracker windows fish basket panel apear when the classify window is not
visible
The speed buttons enable fast operations. Pointing at them trigger the hint function that
explaining their purposes. If auto store is checked, each track generated manually or
automatically will be put in the basket. If not checked one can put a newly generated track
into the basket by pressing the speed button with a fish head pointing into the basket. If one
regret, one can use the button with the fish head pointing out of the basket or the upside
down basket to take out one or to take out all targets put in the basket.

The fish button with question marks opens the classify window while the fish with an
arrow export the content to clipboard or file. The button with a half open lid let you look
into the basket to study the contents (see chapter 14). The pointing hands will bring up the
first prev, next or last track and display it all available windows that can display tracks.
E.g. the echogram, posigram and track information window.

Storing tracks
Tracks generated automatically or manually are stored automatically if the Auto store
checkbox in the tracker or classify window is checked on.
For manual storing either
 Press the speed button with the fish head down in the Tracker or in the Classify
window.
 Press the space bare when the echogram window is active.

Deleting individual tracks

To take tracks out of a fish basket do
 Press the speed button with the fish head up in the Trackers fish basket panel or
 Press the U-key when the echogram is activated or
 Open the fish basket, click at the row for the track to be deleted and press the
Delete-key.
Deleting all tracks
Pour out all tracked targets from the basket.
 Press the delete-key or

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 Press the speed button with the upside down basket in the Trackers fish basket
panel

See also the echogram windows menu Tracking control menu described in chapter 6-
Echogram, chapter 13 classification and 14 fish basket for more information.

Adding and removing echoes in a track

A set of menu items with short keys are found in the echogram window's Tracking control
menu. The items are dedicated to control and ease the tracking The fastest way to perform
manual tracking is to combine echoes with the mouse and apply the keyboard to add and
remove echoes, store and delete track and to toggle between auto and manual tracking.
If the track is surrounded by noise or by echoes from nearby tracks, selecting all echoes
from one track in one operation can be impossible. Select only one or a few echoes in the
first operation. More echoes can be added to the track by pressing the A-key and drawing
another rectangle or by pressing the P-key, move the mouse to the next echoes to add,
press the left mouse button down and point with the mouse at all echoes to be added. An
alternative is to press the M-key to turn the auto tracker on temporarily and draw the
rectangle around all echoes in the track. The surrounding echoes may then be omitted and
the track may be correctly combined in one operation.
 Press A-key to add by drawing another rectangle
 Press P-Key to add by pointing
 Press O-key to remove last added echo
 Press Space-key to save the track
 Press U-key to remove saved track
 Press M-key to toggle manual and automatic tracking.

These keys are short keys to items in the echogram window's Tracking control menu
described in chapter 6. See also the section: Analysis started with the mouse in the
echogram and Selecting echoes with a rectangle in chapter 6.

Display stored tracks

If the classify window is seen on the screen, ensure that the correct basket are selected in
its basket list box.

Alternative 1 Goto first, prev, next and last

If the trackers fish basket panel is visible, use the pointing hand speed buttons. If not,
activate the echogram window by clicking on the echogram's caption and:
 Press Ctrl+Alt+F to see the first stored track in the selected basket
 Press Ctrl+Alt+N to see the next stored track in the selected basket
 Press Ctrl+Alt+P to see the previous stored track in the selected basket
 Press Ctrl+Alt+L to see the last stored track in the selected basket

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These keys are short keys to items in the echogram window's Tracking control menu
described in chapter 6. They provide fast access for browsing trough the stored tracks. The
echogram window must be activated for these keys to work.

Alternative 2 Select track in the fish basket

In the classification window, double click on the fish basket containing the tracks to
display. This will open the basket. In the basket's track statistic page, each track is
represented with a line in a grid. Single click on a line to see the track in the echogram and
in the position diagram window. Double click on a line to see information about the
individual echoes in the track. Double clicking activates the Track information dialog
described in chapter 9.

Alternative 3 Replay the content of a fish basket

Select a basket and then select replay in the classification window's popup menu. (Press the
right mouse button to activate the menu) All tracks in the basket will be presented one at a
time. The classification window's top slider can control the presentation speed. Moved to
the left, the presentation speed will slow down. To temporary stop the presentation, the left
mouse button can be pressed down at the classification window's caption. The process
continues when the mouse button is dropped. More permanent pause is achieved by
pressing the stop button in Sonar5's main menu. This enable the operator to evaluate and
edit the track displayed when the stop was pressed. To continue the replay, select the
replay-continue menu in the classification window's popup menu.
This is further described in the section Replay /Re-classification chapter 13.

Restricting tracking to layers

Pelagic and bottom layers can be applied to restrict tracking to specific parts of the
echogram.

In addition various erasing methods can be applied to erase echoes not to be tracked.
a) Place a layer around the echoes from a stationary target such as a stone in a river
and select the Echogram menus erase SED in visible part of layer will remove
echoes from this stone.
b) Track unwanted targets and press Alt E (Short key to the Echogram menu Erase =>
Erase SED in last tracked target)
c) Track and store unwanted targets in a fish basket. Use the classification windows
popup menu to erase these SED in the SED-echogram according to what have been
tracked.

I need help to get the tracker to track correct

Adjusting the tracking parameters so that all tracks are well detected can be a difficult task
if there are a high density of tracks, the tracks are surrounded by noise or if there are many
missing detections in each track. Situations exists where auto tracking do not work.
a) First one should regard the SED echogram and compare it with the Amp echogram if
this is available. if the track quality is low and or the noise level is high one should
consider to redo the SED-detection or to apply the Crossfilter detector to generate a

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new SED echogram better suited for tracking.

b) If satisfied with the SED echogram, the Track performance dialog and the Auto
parameter detection algorithm can be a great help as described in the section: Tracking
performance dialog.
c) The result from the auto detector may have to be trimmed manually after it has
finished. This is best done with the aid of the tracking performance dialog.
d) If still not satisfied, one can go in to the echogram and erase echoes seen to disturb the
tracking. Press E-key in the echogram window to do so. (See the echogram menu) .
e) One can track all the files and then edit or delete incorrect or unwanted tracks with the
tools found in the classification and fish basket windows.
f) Dividing the echogram into layers and then trim the tracker's parameters to deal with a
minor part of the echogram is a possibility.
g) The last suggestion for tracking of very difficult files is to apply image tracking or
enable other methods described in the image analysis chapter.

Tracking performance dialog

Figure 167. Tracking performance dialog presenting a track predicted by the alpha beta
predictor adjusted with alpha= 0.2 and beta=0. This track is well within the applied gate
in the range domain, but the dialog warns that the track will not be accepted due to the
selected ping gap at this range.
See the section: Charts, in chapter 2 for a general description of the chart.
Optimal adjustments
Optimal adjustment of the advanced tracker may not be a trivial task when there are high
densities of tracks, if the tracks are surrounded with noise or if there are many missing
echoes in the track.

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The tracking performance dialog is one tool that may assist the operator in tuning the
tracker. The dialog displays the actual and predicted echo positions together with the
applied gate graphically and numerically. One and one dimensions can be studied at a time.
In addition, a warning window will indicate why and where a track eventually is not
accepted.
The dialog tests all settings except for the association. Association has to be tested with the
auto detect algorithm or by studying the auto tracking result.
Preparation
Set the tracker in manual tracking mode by checking of the auto tracking checkbox in the
SED-trackers control panel.
Presenting a track to the performance dialog
Draw a rectangle around the track to test in the echogram window and study the effect.
Alternatively tracks can be taken from the fish basket.
Adjusting the tracker
Study the effect in the different domains and tune the tracker's parameters. For each
change the track has to be presented again.

Automatic parameter detector

Preparation
Manually track and store a representative set of fish tracks. The basket(s) where the tracks
have been stored is regarded as a training set. Select the baskets to be applied, and press
the auto-parameter detection button.

Detecting parameters for the Track supporter

The detector will analyze all the stored tracks. Ping gap and track length is measured
individually for all defined steps in the stepwise track-length and Ping gap function. For
track length this is done for each of the three available track length measures. The results
are stored for each measure and the best fit is presented.

Detecting parameters for the gates and predictors

The gates are trimmed to give an optimal fit to the analyzed tracks. The fit will vary
between each of the four predictors. The best fit for each predictor is stored. The overall
best fit is presented together with the predictor resulting in this fit. Manually selecting
another predictor will automatically change the gate and present the resulting best fit with
this predictor.
Since all possible parameters for each of the four predictors has to be evaluated, the
process may take some time to carry out if many tracks have been added to the fish baskets
(training set).
The predictor that gives the smallest gate for all tracks in the training set is regarded as the
best.

Detecting weights for the association

The association weights are determined as the inverse of the uncertainties detected in the
different domains. A high uncertainty value gives a low association weight.

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Crossfilter tracking
Please see the section Step 3 Crossfilter tracking in chapter 19.

Demonstrating the effect of various alpha beta parameter

settings
The charts below have been produced by the tracker's performance dialog, accessed by the
performance button. Upper and lower gate has been hidden during the test.

Alpha=0, Betha=0

Alpha=1, Beta=0

Alpha =0, Betha=1

Alpha=0.5, Betha=0.5

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Alpha=0.3, Betha=0.1

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Main menu

ABOUT CLASSIFICATION ........................................................................................................................................314

POPUP MENU ..........................................................................................................................................................315
Help ..................................................................................................................................................................315
Classification ...................................................................................................................................................315
Tracking ...........................................................................................................................................................315
Baskets .............................................................................................................................................................316
Echoes ..............................................................................................................................................................316
Save all baskets ................................................................................................................................................316
Load all baskets ...............................................................................................................................................317
Advanced Load and save ..................................................................................................................................317
Export...............................................................................................................................................................317
Replay ..............................................................................................................................................................317
Alarm on count .................................................................................................................................................317
Annotation to text file .......................................................................................................................................317
WHAT IS A FISH BASKET ........................................................................................................................................317
Opening a fish basket .......................................................................................................................................318
Creating and deleting baskets ..........................................................................................................................318
Selecting baskets ..............................................................................................................................................318
MANUAL CLASSIFICATION .....................................................................................................................................318
Manual classification and manual tracking .....................................................................................................294
Manual classification and automatic tracking .................................................................................................294
AUTOMATIC CLASSIFICATION ................................................................................................................................294
Absolute classification .....................................................................................................................................295
Linear discriminant function classification ......................................................................................................295
Replay ..............................................................................................................................................................296
Classification function classification ...............................................................................................................304
COMPARING TRACK STATISTICS.............................................................................................................................305
DESCRIPTION OF COMPONENTS ..............................................................................................................................305
Wait on user action button. ..............................................................................................................................307
Add track button ...............................................................................................................................................307
Skip track button ..............................................................................................................................................262
Classification speed scroll bar .........................................................................................................................262
Store track checkbox ........................................................................................................................................262
New basket button ............................................................................................................................................262
Basket up or down ............................................................................................................................................263
Comparing track statistics ...............................................................................................................................263
TRACK FEATURES ..................................................................................................................................................264

Background material is found in chapter 14, 9.2.3 Classification and Application

of linear discriminant function..... in Balk (2001), and in Johnson and
Wichern,(1992)

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Main fish basket

list-box

Track feature
list-box

Unwanted fish basket list-box

Figure 168. Classification window

About classification
The purpose of the classification window is to classify and store tracks. Whenever echoes
have been combined into a track by manual or automatic tracking, a copy of the track is
sent to the classification window. Here the track can be sorted into one of the defined
storage devices named fish baskets.

The classification window can be set up to ask the operator for advice on which basket to
place a track in or to make its own suggestions. New fish baskets can be defined or deleted.
Tracks in a basket can be moved to another basket, combined with other tracks or deleted.

The actual classification works by a set of track criteria defined in each of the fish basket.
One basket can be set up to accept large fish while another can be set up to accept tracks
with a certain velocity. Multiple criteria are allowed and criteria can be transformed by
linear discriminant analysis.

The classification-window simply sends a track copy to each of its baskets and asks if the
basket can accept the track. Baskets answering yes will be highlighted in the classification
window and the copy will be stored.

If the "Store track" checkbox is on and the "Wait on user action" button is up, the track will
be stored automatically in the baskets that answer yes. Tracking and storing can be slowed
down by the scrollbar located in the upper right corner. Slowing down the tracking speed
gives the operator time to evaluate the tracking and classification performance.

If the "Wait on user action" button is down the classification window will show a blinking
fish and wait until the operator press the Skip track or Add track button.

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Popup menu

Figure 169. The classification windows popup menu. Pressing the right mouse button in
the classification window opens the menu.

Help
Opens this chapter.

Classification
This sub menu let the operator select between absolute classification (default) and linear
discriminant analysis. If linear discriminant analysis is selected, parameters can be added
and extracted between statistical packages and Sonar5. See the section: Classification.

Tracking
Tracking Window
If the tracker has been closed this menu items will open it again.
Skip Track
Skips a track during Auto tracking / Auto-classification when the "Wait on user action"
button has been pressed down. Same as the Skip track button.
Add track
Adds a track to the selected fish basket. Same function as the Add track button.
Track statistics
Same as pressing the Compare statistic button. Selecting two fish baskets and pressing the
menu option opens the compare statistics dialog.
Goto track
Sub menu that let you inspect the first last, next and previous track in the selected fish

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basket. Use the short-keys to ease the operation. Only tracks from a selected basket will be
presented. Each basket will remember the last presented track.

Baskets
Copy selected basket
Generates a copy of the selected fish basket.
Delete marked baskets
Delete the marked baskets
Merge to first selected
If two or more baskets are selected, this menu option will move all tracks in all the selected
baskets into the first selected basket.
Empty marked baskets
Removes all tracks stored in the marked baskets.
Generate baskets with artificial size distribution
The menu item opens a dialog that let the operator load or writes a TS distribution. The
dialog will then generate a number of artificial fish tracks according to the distribution.
Use statistical software or spreadsheet like excel to generate the wanted distribution.
Unselect all
There are situations when one may want to remove all basket selections. A selection is
indicated with a changed color. Light blue is default. The operating system (Windows)
controls the color of the selected items.

Echoes
This sub menu contains special routines for interaction between tracks and echoes in the
SED and Amp echogram.
Echoes=>Mark SED in the echogram as erased if they exist in selected baskets
Routine 1 will mark single echo detections found in the selected fish baskets as erased in
the echogram. This can be useful for noise cleaning or for highlighting or hiding special
echoes. In a fixed position application stationary targets such as stones on the bottom may
produce very long tracks. Tracking with the tracker set to accept only very long tracks can
fill a basket with unwanted tracks. These can then be removed from the echogram with this
routine. Echoes marked as erased can be recalled, inverted or presented with special colors
in the echogram. Inverting will mark all erased SED as not erased and all not erased SED
echoes as erased. See the echogram control dialogs Erase noise page. This contains the
tools that handle erasing and recalling.
Echoes=>Erase AMP samples before and after each track
Routine 2 was made especially for correcting Amp-echograms from EY500 if Q telegrams
was stored in 40logR. These echograms can normally not be used for echo integration
because a few samples before and after tracks are off axis position corrected. This can not
be corrected and must be erased.

Save all baskets

Fish baskets are stored in files with the extension .FB. a fish basket file can contain one or
more fish baskets. This menu item saves all defined baskets in the same file.

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Load all baskets

Accesses the file open dialog. Files with the extension *.FB. can be selected and opened.

Advanced Load and save

This menu contains additional menu options for saving and loading fish baskets.

Export
The export menu contains sub menus for exporting the content of all selected fish baskets,
fish basket names with counting results and features for the last presented track.

Replay
Replay means presenting all tracks from a fish-basket on by one. Only one basket can be
replayed at a time. Replying can be useful both for visual evaluation and for
reclassification of the stored tracks. (Sorting into other baskets with other criteria)

The popup menu provides three replay items.

 Replay. Starts replaying from the first track.
 Replay (continue) Starts replaying from the last presented track if replay has been
halted by the stop menu.
 Show track when replaying. To gain processing speed when reclassification is the
aim, the presentation of tracks can be suppressed.

Replying can be halted by Sonar5's main menu: Stop.

Alarm on count
Check menu. Gives a sound beep each time a track is accepted by a fish basket.

Annotation to text file

Writes a track note with information about the last tracked target to the memo located in
the Description page of the Advanced sonar parameter dialog. (See Sonar5's main menu:
Utilities - Description of the sonar file) Note that the Advanced sonar parameter dialog
must be open for this function to work.

What is a fish basket

A fish basket is a storing device for tracks. By default, three baskets are defined. These are
named Fish basket, Trashed and Garbage. New baskets can be defined by pressing the
button with a picture of an empty basket. The Classify window shows each basket by
presenting its name as a text line in the windows upper list box. The number in front of the
name indicates the number of tracks stored in the basket. Clicking the name of a basket
will open the basket. A basked can be tuned to accept certain types of tracks. A basket can
present track statistics numerically and as histograms and functions.

As an example, in a case of a horizontal river monitoring project, two baskets can be

defined so that one basket accept upstream moving tracks and another accept down stream

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moving tracks. The classification window can suggest where to place each new track
according to the track's movement. If a track does not fit any of the defined baskets, it will
be placed in the basket named Garbage. In this case, tracks with zero velocity will end up
in the Garbage basket. If a track is deleted from a basket later, it will be transferred to the
basket named Thrashed. Here it can be recovered or deleted forever.

Figure 170. The classification window's fish basket list box with four baskets. All empty at
the moment.

Opening a fish basket

Double-click on the line with the name of the wanted basket in the upper list box opens the
basket.

Creating and deleting baskets

Pressing the "New basket" button generates a new basket. Pressing the right mouse button
in the classification window opens the popup menu. From this menu selected baskets can
be emptied or deleted.

Selecting baskets
Baskets are selected with the mouse. Single click the wanted basket line in the upper list
box does the selection.
Fish baskets are further described in chapter 14.

Manual classification
Manual classification and manual tracking
Assume that two fish baskets have been generated in a river project. One named fish up
and another named fish down. Echoes from a fish have been combined into a track and it is
seen in the position diagram that the track migrates upstream. This is verified by the
classification windows feature list-box by the velocity feature. To store the track in the
basket containing upstream fish, the operators has to single-click with the mouse on the
correct basket and then click on the "Add track" button.

Manual classification and automatic tracking

Assume that two fish baskets have been generated in a river project. One named fish up
and another named fish down and that the tracker generates track automatically. There will
be three kinds of tracks. Tracks from fish migrating upstream and tracks from fish
migrating downstream. In addition unwanted tracks from debris, air bubbles, boat wakes,
and stones on the bottom may be generated.
Click on the "Wait on user action" button so that the button stays in down position.

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Each time the tracker generates a track the red "waiting fish" warning icon in the
classification window will start to blink. Study the track in the position diagram windows,
in the echogram, in the classification windows feature list-box or in any other available
window to determine what sort of track it is. If it is an upstream migrating fish, click on the
basket named Fish up. If it is a track from a downstream migrating fish, click on the basket
named Fish down. If it is an unwanted track, click on the basket named garbage or click on
the "Skip track" button marked with a basket and a x.

Automatic classification
The fish baskets are the engines in the automatic classification system. Each fish basket
has a track filter page displaying the features selected in the feature library. For each
feature a track criterion can be set. All defined track criteria have to be met for a basket to
accept a track
There are three different ways to use the track feature and the classification filters.
1. The absolute classification is simple and works best with one or a few criteria.
2. Discriminant function work best with two classes and more than one criterion.
3. Classification function works fine with multiple classes and more than one criterion

Classes and fish baskets are synonyms in this context.

p c2
Mixed c3 Fish up
c1 Debris
class absolute demand
absolute demand
x < -0.2 x > 0.2

x=Velocity

-0.2 +0.2

Figure 171. Two calsses of tracks with partly overlapping distributions.

Absolute classification

Figure 172. Example of a fish basket with an absolute demand on the velocity feature. In
this case the demand is not fulfilled since the track is moving with positive velocity. This
basket will not accept the track.

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Preparations in the classification window

1. Define as many fish baskets (classes) as needed by pressing the New basket button.
2. Select "Abs. demand classification" in the Classification window's popup menu (Figure
173)
3. Double click on each of the new fish baskets to open them.
Preparations in the fish baskets
When the basket has been opened:
1. Give the basket a name according to the class of tracks it is supposed to represent. E.g.
Fish up, Large fish, Fish down. Debris, Stones.
2. Open the baskets Track filter page and define the absolute demands in the third, fourth
and fifth column as described below.

The column labeled " = = =  IN" defines the operator to be applied. For the
operators , =, =, =, and  The first Abs. value column holds the operand. The track
feature will be compared with this value according to the operator. For the operator IN
both the Abs value columns are applied. The first holds the lower bound, while the second
holds the upper bound. The nop operator is applied by default. This is a shortage for No
operator, which means no track filter applied for the feature on that line.

Linear discriminant function classification

Replay
Replay means presenting all tracks from a fish-basket on by one. Only one basket can be
replayed at a time. Replying can be useful both for visual evaluation and for
reclassification of the stored tracks. (Sorting into other baskets with other criteria)

The popup menu provides three replay items.

 Replay. Starts replaying from the first track.
 Replay (continue) Starts replaying from the last presented track if replay has been
halted by the stop menu.
 Show track when replaying. To gain processing speed when reclassification is the
aim, the presentation of tracks can be suppressed.

Replying can be halted by Sonar5's main menu: Stop.

Figure 173. The classification window's popup sub menu: Classification.

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Assume that three baskets have been defined in a Salmon-river monitoring project. Fish
up, debris and noise. One would think that setting criteria on the track velocity feature
should be sufficient to separate the three classes. Fish up with upstream velocity, noise
with zero velocity and debris with down stream velocity. However, this is not so. An
automatic tracker can generate tracks from noise echoes with both upstream and down
stream velocity. It is also possible that phase signal in a river can be disturbed so that
overlap in the distribution of tracks from fish and debris occur.
Applying more features such as TS, variation in TS, position in the river, and smoothness
of the track can then improve the classification. Each of these track features contains some
explanatory power, but solemnly, none of them are able to separate the three classes.
It is possible to find a linear combination of the features that separate different classes
optimally. Each feature in a new track is multiplied with a factor and the results from all
applied features are summed. If the factors are defined correct the sum will be better suited
to separate the classes than the individual features.
Preparations
1. Define as many fish baskets (classes) as needed by pressing the classification window's
"New basket" button.
2. Select "AbsDemand classification" in the Classification window's popup menu. See
Figure 173
3. Double click on each of the new fish baskets to open them. Set the name and close the
basket.
4. Build up a training set. To do so, tune the auto tracker if auto tracking is to be applied.
Then perform a "Manual classification of automatically tracked fish" (see section
above) and store a representative set of tracks in each of the defined baskets. If manual
tracking is to be applied perform a "Manual classification of manually tracked fish"
(see section above) and store a representative set of tracks in each of the defined
baskets.
5. Select "Copy Discriminant classification" in the Classification window's popup menu.
See Figure 173
6. *Paste the copied features and class names into a statistical package capable of
performing multivariate statistical analysis. The pasted table will contain a line for each
track with all features and ending with the class name. Separator between columns are
tabulators
7. Use the statistical software to select the features that separates the classes best and find
the discriminant function factors.
8. **Open one of the fish baskets and select the feature library from the baskets top menu.
Select the features found in the multivariate analysis. Select also the feature named 65-
Discriminant function near the bottom of the library.
9. **Open the fish basket's track-filter page and write the obtained factors in the factor
column.
10. In the row labeled Discriminant function, set a track criterion to separate this class /
fish basket from the other fish baskets. The value to be applied as a criterion can be
found from the multivariate analysis. It can also be found by applying the Compare
statistics method described in this chapter

*The format of the copied table has been specially designed to fit Statgraphic PLUS 4.0
**Step 8 and 9 can be carried out as one fast past command if the discriminant function
has been copied to clip board. To paste the factors and select the correct features, select the

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basket and select the popup menu "Past discriminant function coefficients to selected
basket. The discriminant function must be copied to clip board in the following format:

Feature_19 0.5
Feature_31 0.1
Feature_47 0.7

Table 10. Discriminant function factor table to be pasted to a selected fish basket
Here Feature_19, 31 and 47 referees to the feature described in line 7, 8 and 9 in the
feature library. The text "Feature_" can be any text not containing numbers and space. It is
only the number in the end of the word that identifies the features. The following numbers
(0.5,0.1,0.7) are factors. Both tabulators and space can separate the feature indicators from
the factors.
Sonar5 is now ready to classify tracks by discriminant function analysis. If manual
classification is applied, the classification window will suggest the basket to put the track
into. With automatic classification, the track will be stored in the suggested basket
automatically.

Figure 174. A fish basket set up to perform discriminant function classification. The
discriminant function feature is the same as Y in Figure 175.
x2 x2

Old distributions

New distributions x1
y

R1 R2

Figure 175. The discriminant function factors can perform a linear transformation of the
original feature x1 and x2 into a new feature Y. The explanatory power from x1 and x2 has
been concentrated in Y. Y is the same as the discriminant function feature seen in Figure
174. Clearly setting a criterion on the Discriminant function feature Y will separate the
classes better than setting criteria on X1 and X2

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Classification function classification

This method is similar to the linear discriminant function classification method except that
the discriminant factors are developed to give a sum score function. The Discriminant
function feature is not applied and no demand has to be set. Each feature are multiplied
with its respective factor and summed. With manual classification, the fish basket resulting
in the highest sum score will be suggested. With automatic classification this basket will
win the track.
The method works well with multiple classes and multiple features, and it is simpler to set
up than the discriminant function classification. To set up Sonar5 to perform this
classification, follow the steps given for discriminant function classification in the
preparation section with the following exceptions:
4 select discriminant classification and not AbsDemand classification
7 develop the sum-score factors and not the discriminant function factors
9 skip the last part about selecting the discriminant function feature
To simplify the setup of the baskets, paste tools have been implemented. If a table similar
to the one seen in Table 11 is copied to clip board, and the "Past classes and classification
function coefficients from clip board" menu in Figure 173 is selected. Three new fish
baskets (classes) with the name 1, 2 and 3 will be generated. Feature number 14, 26, 31, 39
and 44 will be selected in the feature library. And the factors in each of the new fish
baskets will be set up according to the factors in the table.

1 2 3
Col_14 0.314914 0.505118 -0.215994
Col_26 -0.400821 0.937849 -0.179973
Col_31 -0.37246 0.221706 0.807988
Col_39 0.712493 0.847118 0.337072
Col_44 0.317756 -0.420308 0.58104
Table 11. Classification function factors clipped from Statgraphic PLUS 4.0

Comparing track statistics

Figure 176. Comparing track statistics.

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Statistics from two fish baskets can be compared. To do so, select two fish baskets
with the mouse in the classification window's upper fish basket listbox and press the
compare statistics button. Click a line in the dialogs lower list box to select a feature to
compare. Use the charts top panel to control the chart's appearance. Use the Settings page
to control the statistics.

Description of components

Wait on user action button.

This is an On / Off button. If pressed, it stays down until next
time it is pressed. When down, the "Store track" checkbox will
be on. Each time a track is generated, the system will wait until
the operator press the Skip track or add track button. Combined
with auto tracking, this function let the operator check and
overrule the automatic classification in an effective and simple
way.

Add track button

When a track has been generated, pressing this button will add a
copy of the track to the selected basket (s). Baskets are selected
automatically by the classify window, but the selection can be
overruled by the operator. To do so, single-click the wanted
basket-name. Then press the "Add fish" button. If the echogram
window is active, pressing the space-key does the same as
pressing this button.

Skip track button

Pressing this button will skip the track and let the auto tracker
generate the next track. Skipped tracks will be stored in the
trashed basket.

Classification speed scroll bar

The scrollbar located in the upper part of the classification
window controls the tracking speed. With auto tracking, one may
want to evaluate the tracking performance "on the fly". It can
then convenient to reduce the tracking speed to get time to
evaluate each track. Moving the scrollbar to the right reduces the
tracking speed. See also replaying tracks in the section
describing the replay menu

Store track checkbox

If checked tracks will be stored automatically in the baskets that
accept the tracks.

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New basket button

Pressing this button generates a new fish basket.

Basket up or down
Pressing these buttons moves the selected baskets from the upper
listbox to the lower or viceversa. This can be useful to rearange
the order of the baskets. Baskets in the lower listbox will not be
applied in the classification process. Tracks in fishbaskets placed
in the lower listbox can be applied as filters for the tracker.

Comparing track statistics

Select two fish baskets and pressing this button will open the
compare track statistics dialog.

Track features
To classify tracks, track features like speed and size are calculated from the echoes in each
track. When the Classification window receives a track, the features selected in the feature
library are presented in the classification window's track feature list box. The library can be
accessed by double clicking a line in the classification windows center list-box or from the
programs main menu Utilities-System configuration. See the section: Track feature
library in chapter 11.

Figure 177. The classification windows track feature list box presenting the features for
five features selected in the feature library in this example.

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Main menu

ABOUT FISH BASKETS ............................................................................................................................................327

OPENING FISH BASKETS .........................................................................................................................................327
STORING TRACKS ...................................................................................................................................................328
TRACK STATISTICS PAGE .......................................................................................................................................329
Commands and operations ...............................................................................................................................329
Presenting histograms and functions ...............................................................................................................330
TRACK FILTERS PAGE FOR CLASSIFICATION ...........................................................................................................332
SAMPLE STATISTICS PAGE ......................................................................................................................................333
MISC PAGE .............................................................................................................................................................333
EXPORT .................................................................................................................................................................334
Option button ...................................................................................................................................................334
Export angles between neighbor tracks ...........................................................................................................334
Export DIDSON curvature ...............................................................................................................................335
REPLAYING TRACKS ..............................................................................................................................................336
TOOLS MENU .........................................................................................................................................................314

About fish baskets

Fish baskets serve three purposes. They store tracks, they generate track statistics and they
are important elements in the classification system. When the operator combines echoes
into a track in the echogram or when the auto tracker generates a track, the track is sent to
the classification window. The classification window simply presents a copy of the track to
each of the user defined fish-baskets. The baskets can accept and store the track copy or
they can refuse. If a track is refused by all the baskets it is placed in a system defined
garbage basket.

Opening fish baskets

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Figure 178. The Tracker window (left) can hold one fish basket while the Classify
window(right) can hold many fish baskets. The fishbasket panel in the tracker window is
invisible while the the classify window is visible.
It is the classification window that owns and maintains the fish baskets. For simpler
tracking processes when classification is not needed, the classification window can be
closed to make the screen more tidy. If closed, the upper fish basked listed in the classify
window will be transferred to the trackers fish basket panel. If the classify window is
opened again, the trackers fish basket panel will disappear and the fish basket will be
transferred back to the classify windows fish basket list. The fish button with two question
marks opens the classify window.
To open and the actual fish basket, either
 double click one of the listed fish baskets in the Classify window,
 or click the Look into the basket button in the tracker window.

Storing tracks
First manual or automatic tracking must generate a track. The track is sent to the
classification window. The classification window holds the track. If the classification
window has been set up to perform absolute classification (default) then a basket can
refuse to take the track. If (1) "The store track" checkbox in the classification window
has been checked before the track was generated, or (2) if the "Space key" is pressed
when the echogram window is active, then a copy of the track will be presented to the
defined baskets. Each individual fish basket evaluates the received track copy. If no track
criteria have been defined or if the track is accepted according to the defined criteria, the
track is given a registration number and stored. The operator can overrule automatic
classification of tracks. Independent of the classification method, the basket cannot
refuse to accept a track: If (3) the "Store track" button in the classification window is
pressed or if (4) the "Insert track" button in the fish basket is pressed, the track will be
stored independently of any classification rules. Each stored track can be found as a line in
the track's statistic page. Here it is presented with the track features selected in the feature
library. (See chapter 11)

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Track statistics page

Figure 179. The fish basket's track statistics dialog. Clicking a line in the grid will
present the track represented by that line in the echogram and in the position diagram. The
clicked column represents one track feature. This feature from each stored track will
generate a histogram or a function in the chart if histogram or functions have been
selected in the options menu. Double click to see numerical information for individual
echoes in the track.

Stored tracks are presented in the track statistic page as lines in a grid. 20 tracks can be
presented at a time. Use the page down or page up key to see more tracks if more than 20
tracks have been stored.

Click with the mouse at a cell in the track-statistic page grid will
a) Generate statistics for the feature presented in the clicked column. To see the
statistics, histograms and functions must be selected in the options menu.
b) Present the track seen in the clicked row in all open windows such as position and
echogram windows.

Double click in a cell will do the same but will also open a track information window and
present the individual echo positions for the clicked track

Commands and operations

Editing tracks
It is possible to edit tracks stored in a fish-basket. By dbl. clicking the line in the fish-
basket window describing the track, a copy of that track will be created. If the sonar-file
where this track was detected, is available, the track will be showed in the echogram-
window and changes can be made to the track-copy by using the P,A and O-key functions
in the echogram-window. Because all changes are done to the track-copy only, the original
track has to be deleted and the copy has to be inserted in the fish-basket before finishing
this operation.

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Commenting individual tracks

Each individual track can be commented. A fish basket with commented tracks can be sent
by email and opened by other persons to discuss the commented tracks. This has been a
useful feature for training people to interpret echograms and for discussions about strange
echo phenomena.

To comment a track, select the comment feature in the feature library (See the top menu).
The track statistic page will then present a column marked comments. Single click in a
comment cell will open the comment dialog where one can write or edit comment.
Delete all tracks
Press the Del-key. (The track will be moved to the Trash-basket)
Undo delete:
Press the Ins-key. (Takes the track back from the Trash basket.)
Show next track
Press Arrow down - key.
Show previous track:
Press Arrow up -key.
Insert new track from echogram.
Create a track in the echogram window using the mouse.
Press the Insert button in the Fish-basket window.
Merge tracks together
Select the track to merge to with the mouse. (first column)
Press the Merge button.
Select tracks to merge from (First column)
Press the merge button to finish the operation.
Add all comment to a track.
Select comment in the feature library opened with the fish baskets top menu.
Click with the mouse in the appearing comment column.
Move tracks
Mark tracks with the mouse.
Press Ctrl-X
Place the cursor where you want to move to.
Press Ctrl-V
Copy tracks
Same as Move tracks but with the Ctrl-C button.
Goto track button
Set a track number in the number edit box to the left for the goto button. Then press the
button.

Presenting histograms and functions

All track features can be presented as histograms and as functions of other features. Select
Show histogram and function will enable this. When selected, a chart and a control panel
will appear. The control panel controls the histogram and function generation and present
also mean values for the selected features. Features to be studied have to be selected in the

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Feature library. Only selected features will be displayed in the Track statistic grid. Clicking
a column here selects the feature to be handled and presented by the histogram or function
chart. The values that make up the histogram and function can be presented in a separate
memo box. his box is opened with the Menu: Options => Show histogram and function
values.

Figure 180. The options menu opens the histogram and fuction
Histogram and function control panel

Figure 181. The statistic control panel is loated at the left side of the chart when the Show
histogram and function chart has been opened from the Option menu .
Filter size
Histograms can be filtered to clarify the overall trends. Increase the filter size value to
increase the filter effect. 1 does not give any effect.
Chart commander
Check off the chart commander to increase the size of the chart. When checked on, the
commander enables the operator to customize the chart presentation.
Autoscale
Detects the min and max value in the feature selected for presentation and adjust the size
bins according to the user-selected number of points. When off, the operator can set the
bounds manually by altering the From / To values.
Nr. Points
Defines the number of size bins to divide the distributions into.
Mean and standard deviations
Pointing with the mouse at a column in the track grid and clicking once with the mouse
will calculate and present the mean and standard deviation of the track features.
Arithmetic mean label
This label is an active label. Click on the label to open the system configuration dialog
where arithmetic or logarithmic calculation can be selected. The label will reflect the
choice.
When the label says "Arithmetic", logarithmic features such as TS will be transferred to the
linear domain before mean and std. dev are calculated. When the label says " Logarithmic",
mean and std. dev. will be calculated directly from the logarithmic values. A discussion
about log or arithmetic mean is presented in Lilja et al., (2000).

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Histograms

Figure 182. A histogram presenting the size distribution of 51 fish counted in lake d
Annecy.
To generate a histogram, select Histogram in the statistic control panel and click with the
mouse on the wanted feature column. More features can be selected in the feature library
accessed from the fish baskets top menu.

Functions

Figure 183. Two track features can be presented as a function. Here size is presented as a
function of range It is clearly seen the two size groups observed in Figure 182 are located
in two different layers.
Presenting a track feature as a function of another track feature can be useful. Size, ping
gap, track length, and swimming velocity can for example be studied as a functions of
range. To do so, select function in the statistic control panel's page as seen in Figure 181.
Select "Set x-axis" and click with the mouse in grid at the column presenting the feature to
be presented along the x-axis. Select "Set y -axis" and click in the grid to select feature for
the y-axis. The chart will now plot the function according to the remaining control
parameters in the control panel.

Track filters page for classification

Figure 184. Track filters are the engines in the classification.

The first column in the Track filter page presents the features selected at the moment in the

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feature library. To see other features, open the library and select the features. The second
column presents the actual features of the last added track before the basket was opened.
The feature is not updated when the basket is open since all features are available in the
track statistic page.

The three columns following after the Track column does absolute classification. The
column marked with operators defines the operator to be applied in the filter for a specific
feature. For the operators , =, =, =, and  The first Abs. value column holds the
operand. The track feature will be compared with this value according to the operator. For
the operator IN both the Abs value columns are applied. The first hold the lower bound
while the second hold the upper bound. By default the nop operator is applied which is a
shortage for No Operator.
A track has to be accepted by all the defined rules to be stored. If all operators are
nop, no rules are applied. A set of features can be combined into one classification rule.
Setting the factors in the Factor column does this.
See Manual and Automatic classification in chapter 13. Background material are
found in section 9.2.3 Classification in (Balk, 2001)and in Johnson and Wichern,(1992)

Update SED stored in tracks according to the SED-echogram

This menu will redetect SED features such as range, echo length, gain comp, TSc, Tsu, and
PhaseDev for all echoes stored in all tracks in a fish basket. This may be of interest in
cases where the Amp echogram has been smoothed by filters etc. The amp echogram
should have sample resolution and the phase file should be available.

Sample statistics page

This page is designed to study statistical variations in tracked targets. Each individual
single echo detection is looked up in the Amp echogram. From the samples found in the
Amp echogram, statistics such as echo length, standard deviation, kurtosis etc. are
calculated. Both statistics and samples can be presented. Not that doing this for a basket
containing many tracks may take time

Misc page
This page contain the track region panel. The All tracks button will detect the outer bound of all
tracks stored in the basket while the Selected track button will do the same but only for the selected
track. The analyze region button will transmit an analysis message for the detected region. The
region can be edited manually.

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Export

Figure 185. Export. Clicking the Export menu presents the export control panel. Pressing
Go will start the export.

Option button
Press the option button to specify what and how to export. The option button will open the
system configuration dialog’s general page, and mark the important panels with the
important color. When the options have been selected, press the Go button to generate the
export. This will open a message dialog showing the start of the export and asking whether
you want the export to clipboard, file or to be cancelled.
Terminology used in the option dialog
Track features are features calculated from the tracked echoes and from additional data
surrounding the echoes. Selected track features means track features selected in the feature
library. The feature library is located in the system configuration dialog. It can be accessed
with the fish baskets top menu named feature library, pressing F9, by the systems utility
menu or by clicking a feature in the classification window. Echo information means
information about each individual echo. Sample values mean the samples in the Amp
echogram that forms the individual single echoes.

A track feature may differ

Some track features are based on information not stored in the fish basket such as sample
data from the Amp echogram, Motion data from a motion sensor, bottom detections in the
bottom file etc. If a fish basket is saved and reopened, the features will be recalculated and
if the files are not available or if the files have been changed, the features will also
changed. If the bottom has been redefined then target depth will be different from earlier.
If the bottom file has been deleted, then target distance from bottom cannot be estimated.

Export angles between neighbor tracks

This export will calculate the angel between the x, y, z velocity vectors for two and two
tracks.

Track 1: V1=(vx, vy, vz)

Track 2: V2=(vx, vy, vz)

The vectors are normalized to have unit length 1.

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Dot product is calculated. dp =V1 dot V2

Angle = arcos(dp)

Example of export: .

Track nr Angle between tracks (deg)

1.00 2.00 15.85
3.00 4.00 57.06
5.00 6.00 124.40

The export was implemented for Dr. Georg Rakowitz from the University of Vienna in
order to study fish behavior before and after an event such as discovering an approaching
trawl. (Rakowitz et al 2011). Prior to the export each fish had been tracked twice, first
before reaction, and second after reaction resulting in paired tracks.

Export DIDSON curvature

(Experimental method not fully tested.)
The picture of a fish seen in one frame from the DIDSON is regarded as one echo. The
picture of the fish from the next frame is the next echo. If they are tracked we get a track
containing of two echoes. An echo from a split beam echo sounder contains Intensity,
range, along ship and athwart ship measurements. An echo from DIDSON miss the along
ship angle information but has one or more intensity, range, and athwart ship registrations.
The range, athwart ship registrations can be recalculated into x, z coordinates from where
the curvature for each individual echo can be found. Curvature will not be meaningful if
manual tracking with straight lines have been applied.

The algorithm calculates the curvature in three different ways and export the curvature for
each individual DIDSON echo. If a fish has been tracked in three frames (pings), then the
track consist of three echoes and the algorithm will output according to the following
example.

DIDSON TRACK CURVATURES

Reg nr Ping Curv 1 Curv 2 Curv 3

3.00 261 0.00700 0.00194 0.00058
3.00 262 0.00777 0.00168 0.00002
3.00 263 0.00942 0.00441 0.00052

Curv 1 is an experimental formula that may be changed later.

Curv 2 is the average of the mean sum of squares between all points and a linear best fit
line through the points.
Curv 3 is the average of the second differential from all points along the echo.

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Figure 186. One echo in the DIDSON frame viewer. We can see that the line through the
echo is slightly curved.

Replaying tracks
All tracks in a basket can be presented one after the other by replaying. See the replay
function in the classification window.

Tools menu

Figure 187. Items in the tools menu.

Track and file statistics
Presents and copy to clip board statistics for the echogram file and the fish basket. The following is
an example

Fishbasket..........Perch
Filename............Annecy Fr\09292220y7.uuuQ

File statistics
-------------------------
No. of Ping in file..................... 861
No. Ping pr.sec......................... 6.2774
No. SED detections...................... 4362
No. SED detections pr. Ping............. 5.0662

Track statistics
------------------------
Total number of echoes in all track..... 4152
Total number of tracks.................. 164
Average number of echoes pr track....... 25.3171
Average number of tracks pr ping........ 0.1905
Sum missing echoes in tracks............ 289
Average number of missing echoes........ 1.7622
Track Signal to Noise Ratio (TSNR)...... 0.0674

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Track Quality (TQ)...................... 14.3172

Detection probability (DP).............. 0.9349

Track echo info

Opens the track information window and present the selected track. Double clicking a row in the
fish baskets track statistic page does the same as this menu. The track info dialog may appear
behind the fish basket dialog. If not seen, move the fish basket dialog.
Sort tracks
Tracks can be sorted on time, or according to selected feature. Click the column for the wanted
feature in the fish basket’s track statistic page before selecting the appropriate sort menu.
Renumber all tracks
Each track is registered with a number seen in the RegNo feature column. When tracks are
merged, inserted or deleted, moved or copied, it may be wanted to renumber.

Update SED stored in tracks according to the SED Echogram,

Tracks contain copies of the SED from the SED echogram. If changes have been applied to
the SED’s in the Echogram, one may want to update the SED in the tracks.
Copy SED quality marks from echogram to tracks
Individual SED in the SED echogram can have quality marks. Tracked targets will get copies of
these marks at the moment of tracking. The quality definition can be changed for the SED
echogram after the tracking. If so, the new quality definition can be copied into existing tracks with
this menu.
Merge all tracks into one long
All tracks in a basket will be merged into one long track.

Remove echoes that exist in other baskets

The called routine will look through all baskets found in the classify windows upper list
box and check if any echoes in the open fish basket is registered elsewhere. If found in
another basket, the echo will be deleted from the fish basket that called the routine. If all
echoes in a track are deleted, the track will also be deleted. Once started, the deleted
echoes can not be recalled. The method can be useful e.g for getting an overview of not
tracked echoes. One will then first track targets and place them in different baskets. Then
track all existing echoes into a separate basket and then ask this basket to remove echoes
that exist in other baskets. This will result in a basket that show what has not been tracked.
To highlight echoes that have not been tracked in the echogram, see the classify windows
popup menu: Echo=> Mark SED in the echogram as erased if they exist in selected
baskets, described in chapter 13.

Split tracks into single echo tracks

Tracks with more than one echo will be split up into individual tracks with one echo each.
Track features in the fish baskets are average numbers based on all the involved echoes in
a track. This method is useful in cases where one want to study and export track features
for each individual echo. It can also be applied if one wants to use the single echoes in a
fish basket to establish the size distribution for biomass estimation.

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Main menu

About image analysis ................................................................................................................................. 340

IMAGE COMMAND EDITOR ............................................................................................................................... 340
How to do it ................................................................................................................................................ 340
START AND STOP BUTTONS .............................................................................................................................. 341
ESSENTIAL DETAILS ......................................................................................................................................... 341
Detail 1, the color look-up table (LUT) ..................................................................................................... 341
Detail 2, the base threshold ....................................................................................................................... 341
Detail 3, image buffers ............................................................................................................................... 342
Detail 4, disk space and virtual memory .................................................................................................... 342
Detail 5, border effects and filter sizes ...................................................................................................... 342
Detail 6, regions, objects, detections samples and tracks .......................................................................... 343
Detail 7, parameters .................................................................................................................................. 344
Notes and advises ....................................................................................................................................... 344
Working with multiple files ........................................................................................................................ 344
IMAGE ANALYSIS COMMAND WRITER .............................................................................................................. 345
IMAGE ANALYSIS COMMANDS.......................................................................................................................... 345
TEMPLATE DIALOGS ........................................................................................................................................ 327
Filter template ............................................................................................................................................ 327
Bottom detector template ........................................................................................................................... 328
Masking template ....................................................................................................................................... 329
Single echo detection template ................................................................................................................... 329
Crossfilter detector template ...................................................................................................................... 330
Crossfilter tracker template ....................................................................................................................... 332
ECHOGRAM ENHANCEMENT WITH LOW PASS FILTERS ...................................................................................... 333
SINGLE FISH DETECTION IN NOISY ENVIRONMENTS .......................................................................................... 333

See also: Programming, Development of a new single echo detector suited for...., Improved
single fish detection in data from split-beam sonar in Balk, (2001) and A new method for
single target detection (Balk and Lindem 2002). Books on image analysis: (Niblack, 1986)
and (Pratt 1991)

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Do not read this chapter

This chapter contains details about image analysis normally not needed for operating
Sonar5. Image analysis is part of Sonar5s engine. It is only when the operator wants to
perform or compose analysis methods not found in the analysis menu that the details in this
chapter are needed.

About image analysis

Image analysis is a powerful tool. It can be used to improve echograms and to assist in fish
detection. Image analysis is implemented as a command language controlled from the
Tracker windows image page. Writing a series of commands in the windows command
editor and pressing the "Start analyze" button does the image analyzes.

Templates are implemented to help the operator setting up the commands. Press the right
mouse button in the Tracker window and select templates to get the templates. The
templates are also accessible from the programs analysis menu: Analysis=Pre-analysis
and from Analysis=1-Setup=Tracking=Image tracking.

Image command editor

Figure 188. The Image analysis page in the Tracker window. Upper memo is the command
editor while the lower memo is the filter coefficient memo.

How to do it
To get an idea of the working principles, open a sonar file and do the following:
1. Open a template dialog. E.g. Analysis=Pre-analysis =Filter
2. Adjust the parameters in the template if necessary

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3. Press the Test job or real job button in the template.

Observe the text appearing in the Tracker windows Image page command editor.

Do also test the command writer located in the trackers popup menu.

Start and stop buttons

The "Start Analyze" button in the Tracker windows Image page starts the image processor.
This reads and interprets each line in the command editor. If a command has been
erroneous spelled or if parameters are missing a warning or an error message will appear.
Some commands will generate analysis messages that will be sent to other parts of the
program. As an example the tracking command will call on the SED-tracker, and this will
again generate and send tracks to the classification unit. In such cases it is important that
all the involved analyzes has been correctly adjusted.

Pressing the stop button will halt the execution at the first possible breaking point.

Essential details
To understand the image analysis commands it is essential to know a few details about
how the program works.

Detail 1, the color look-up table (LUT)

Sonar5 translate echo intensity values into positive integer values ranging from 0 to 1023.
(10 bit) This gives a dynamic of 102.3 dB with a resolution of 0.1 dB. This is well within
the accuracy and dynamic of the echo sounders. These integer values are stored on the disk
in the converted sonar file (.uuu). Operating with integer values increases processing
speed, reduces memory consumption and file size. Another advantage is that we can apply
a look-up table (LUT). The LUT contains the colors to represent the echo intensities on the
screen. Simply applying the echo intensities as indexes in the LUT gives the correct color
to present on the screen. This is extremely fast compared with other techniques where the
color has to be calculated for each sample. Here no calculation is needed. This is the most
important reason to why SonarX work fast even with high-resolution echograms.

Detail 2, the base threshold

When data is represented with positive integer values zero form an absolute minimum
(base threshold). Threshold can be increased, but not lowered. When SonarX convert a file,
a base threshold is set at the initial parameter dialogs Amp-page. Echo intensities having
this threshold will form the base threshold and be assigned to zero integer values. To save
disk space and to optimize read and write processing speed, Zeros are not stored. The
echogram window can raise the threshold, but naturally not lower it. Raising the threshold
is simply a question of changing the contents of the LUT described in previous section. For
every echo-intensity below the raised threshold, the LUT will contain the background
color.

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Detail 3, image buffers

Image analysis works with images. A total of eight images (memory buffers) are available.
They images are

1 WorkImage Operations are carried out on this buffer

2 TmpResultImage Results from an operation are temporarily stored in this buffer
3 ErasedImage Buffer taking care of erased data
4 KeepImage1 Storage memory allocated by the Keep command
5 KeepImage2 Storage memory allocated by the Keep command
6 KeepImage3 Storage memory allocated by the Keep command
7 AloImage Buffer for angular data
8 AthImage. Buffer for angular data
Table 12 Overview of Buffer Images

Most operations do only use the Work, TmpResult and Erased images. They are allocated
by the load command. The other images are allocated only if needed. When the load
command is applied, the requested part of the last activated echogram is loaded from disk
and into the WorkImage. If a processing command is called like “Mean 3 3”, WorkImage
is used for the filtering, while the result is placed temporary in the TmpResultImage. After
the filtering the two are flipped so that the WorkImage then contain the filtered result while
the TmpResultImage contain the image prior to the filtering operation. The Show
command will then show the filtered result stored in the WorkImage. Most commands
operates on the WorkImage except for commands dedicated to work on the angle and keep
images.
TheKeepImages are storage devices. Applying the command Keep will copy the
WorkImage into a KeepImage. This enables storing of an intermediate result. KeepImage
can be combined with a later result in WorkImage. Examples of commands combining
KeepImage with WorkImage are Save, ThresholdAdd, Segmentation and Magnitude.

Detail 4, disk space and virtual memory

The images are loaded into memory. Large high-resolution echograms are normally bigger
then the available memory. To solve this virtual memory are applied. The part of the
images not used at the moment is swapped to disk. There has to be more than three times
the disk size free on the local C-disk. A sonar file of 1MG may need more than 3MB disk-
space to be processed if all images are applied.

Detail 5, border effects and filter sizes

Operation applying convolution of matrixes will result in border effects. As an example,
Mean 5 3 will not be able to process the 2 upper and lower rows of samples (5-1)/2, It will
also not be able to filter the 1 and last ping. (3-1)/2. To avoid moving targets in space
commands applying convolution should always be assigned odd dimensions such as 3x5,
5x9 and 3x1, and not even dimensions such as 4x2. The reason is that these operations
produce center samples.

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Detail 6, regions, objects, detections samples and tracks

What is samples
The Amp echogram consists of samples. When the returned echo energy is received by the
echo sounder, the high frequency component (e.g.120 kHz) is removed in the Amplitude
detector. The remaining low frequency variations contain the echo information. This
information is cut up in samples with a sample frequency between 10 and 30 kHz.
Depending on the sample frequency and sound speed, each sample covers a few cm of
water in the range domain. When successive pings are treated, the resulting samples are
organized in a matrix with samples from the same range in the same row (range bin) and
with successive pings forming columns.

Detected region or object

Definition: A detected region or object is a cluster of samples with values different from
Zero, surrounded with zeroes on all sides. An example is seen in Figure 189.

Assume that all samples have a value above the base threshold described in Detail 2. Then
the contents of the matrix may be regarded as one continuous surface. The object or
detected region will be the entire matrix with the shape of a rectangle. The perimeter length
is found by counting all samples along the perimeter of the matrix. An echogram
containing 100 ping and 250 samples will have a perimeter with length 99 +249 +99 +249
measured in samples.

Assume that we threshold the echogram so that only samples from one fish remains
unaltered in the Amp echogram while all other entries are assigned to zero. The samples
that differ from zero form a region. This region has another, but still well defined
perimeter. The size of the region can be measured in number of samples along the
perimeter. It can be measured in width as the number of pings from the start to the end of
the region, in height measured as maximum number of samples in the range domain
spanned by the region, or as area being maximum length times maximum height.

Figure 189. Detected region / object.

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Detail 7, parameters
Parameters can be real values, integer values, letters or words. Parameters are separated
with space in almost all situations. Real values apply the decimal separator noted in
Windows control panel. Parameters enclosed in <> has to be applied while parameters
enclosed in [] are optional. Only one command can be applied on each line in the
command editor.

Notes and advises

The command "Show" presents the results in the Echogram window. However, this result
is not stored and can not be used directly as basis for other analysis. To work further with
the results, they have to be saved in a new file and then opened. The Save commands adds
a Q to the original filenames extension. This separates original and the new file.

Three factors will influence on the result. They are the Range resolution (meter per
sample) the ping interval, and the transmitted pulse duration. The same process can
produce different results when these factors change.

To get good results with the image analysis, Range resolution should be so high that single
fish are seen with 3 samples or more. (Zoom in the echogram to see).

Thresholds introduce discontinuities in the echo signal. To get good results with the image
analysis, sonar files should be converted with an Amp echogram threshold of -100dB.

Always apply odd parameter numbers in filters. Even numbers will move the result slightly
in range and time.

Working with multiple files

The command "next" will close the active file, open the next file in the auto file change list
and restart the image analysis from the first command in the command editor.
Example:
If three files Test1.1U1, Test2.1U1 and Test3.1U1, have been selected in the file open
dialog and the following commands have been written in the image editor.

Load 0 1
Mean 3 3
Save
Next

Each of the three files will be filtered and the result written to three files with the names;-
Test1.1U1Q, Test2.1U1Q and Test3.1U1Q.
If one want to see the processed results at any stage in this process adding the command
Show will do.

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Image analysis command writer

Figure 190. The image command and filter writer

The image command writer is designed to help writing commands designing filters. Select
a command or a filter from the list gives a short explanation and set up a suggested tuning.
Pressing add will insert the command at cursor position in the trackers image editor and
add a filter to the filter editor if filter has been selected.

Image analysis commands

This section contains a description of the image analysis commands. In the command
editor the semicolon sign ; means a comment. In the following section the sign will be
applied to indicate a new line. As an example, Load 0 1; Mean 3 3; Show; Free; has to be
written ........

Load 0 1
Mean 3 3
Show
Free

in order to be understood by Sonar5s the command interpreter. Adding a semicolon after a

command here enables the operator to write a comment. Adding a semicolon in front of a
command will remove the command from the analysis.
ApplyAsBottom <MinR> <MaxR> <Margin > [save]
Example: Load 0 1; BottomDetection 2 100 -70 -12 -12 0.5 0.2 0.00 x; show; mean 1 5;
ApplyAsBottom 2 100 0.00 s; show;
Obtains a bottom line from the first occurrence of echoes above the base threshold in each
ping within MinR and MaxR. Margin is added to the detected range. If followed by an s
the bottom line is saved in the echograms bottom file.

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BottomDetection
<MinR> <MaxR><Threshold> <StartLevel> <StopLevel>
<MinEchoLength> <Min.Search gate> <Margin> [Save]
Example: Load 0 1; BottomDetection 2 100 -70 -12 -12 0.5 0.2 0.00 s
The command involves a multiple target detector and a bottom candidate search algorithm.
MinR and maxR restricts the search. Threshold eliminates candidates weaker then the
threshold, Start level defines the pulse start level in dB relative to the peak value. Stop
level defines the pulse stop level in dB relative to the peak value. Min echo length
measures the bottom pulse relative to the transmitted pulse. Min. search gate defines a
minimum search gate in the range domain. The value is applied when the detection
algorithm compares detections to find the most probable candidate relative to the neighbor
detections. Margin is simply a numbers that will be added to the detected bottom depths.
Save is optional if a letter s is found the result will be saved as a bottom line. The echo
representing the best bottom candidate will be available in TmpResultImage and can be
seen by applying a show command.

The bottom echo can be processed further with other commands.

Example: Load 0 1; BottomDetection 2 100 -70 -12 -12 0.5 0.2 0.00 x; show; mean 1 5;
ApplyAsBottom 2 100 0.00 s
show;

See also chapter 4, section Bottom detection

Break
Halts the execution permanently. Useful when testing series of commands.
ChangeSonarEQ
Parameters: <model>
If the echogram presents TS-values with 40logR TVG, the echogram will be recalculated
to present 20 log Sv values and vice versa.
Comments
Semicolon ";" is used to indicate a comment. When placed in front of a command, the
command will be regarded as a comment and not processed. Marking a set of commands
with the mouse and pressing the comment button will insert a ; in front of the marked
commands. Marking the commented commands and pressing the comment button will
remove the comment mark (;). This is a fast way to add and remove commands from the
processing chain during test. Alternatively a set of commands can be avoided by writing
the word break before the first command to avoid.
CopyToClip board
Extract ping number, range and TS to clip board. Apply this command only after peak or
SED detection. Pasted into a spreadsheet the detected regions can be studied further.
CutRange
Parameters: <MinR> <MaxR>
Example: Load 0 1; CutRange 10 45; show;
Cuts the echogram at ranges shorter than MinR and longer than MaxR.
DetectStone
Parameters: <Method> [Action]
Example: Load 0 1; DetectStone Hist;

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This is an old method investigated in 1998. The command controls a noise dialog. This
dialog is only available in our test versions at the moment. The idea is to search trough the
echogram to detect stationary targets in the beam. In shallow rivers, echoes from stationary
targets such as stones on the bottom can be disturbing. Echoes from these targets can be
detected since they form long tracks in the echogram with very little change in range in
both the SED and Amp echogram. Summing up TS values in each range bin from the Amp
echogram to form a histogram, results in peaks at ranges where echoes from stationary
targets like stones are found. Setting a threshold in the histogram defines the start and stop
range of these targets. The method detects stationary targets and generates baskets named
stone baskets in the lower list box of the classification window. Double clicking a stone
basket will place a pelagic layer around the detections in the echogram window. From the
classification menu, single echo detections found in regions with stones can be marked as
erased. Although the accompanying dialog is not available, the command can be applied
with the parameter “Hist”. No other parameters must be applied at the moment. The future
for this command is not decided.
DrawBorder
Parameters: <Color> [hollow]
Example: Load 0 1; Show; Segmentation 1 3 55 1 -6; show; DrawBorder 500 R show;
Example: Load 0 1; FindObjects 5 55; show; DrawBorder 500; show;
Draws a border around detected regions. The command assume that findobjects has been
called by a previous command or directly and that regions exists.

Color is an index to the LUT defining what color will be applied to show the border. Color
is a value between 0 to 1023. If hollow = R then the internal of each detections are
removed leaving only the border.

Filter
Parameter: <name>
Example: Load 0 1; Show; Filter a; show;
All-round convolution filter. The command reads the filter coefficients labeled "name" in
the image windows lower memo. The filter coefficients decide whether the filter should be
a high pass or a low pass filter. Coefficients are separated with space. In the following
examples a, b, c and d is the name. All filters are 3x3 filters, but other dimensions may be
defined as well. Increasing the size in one dimension will increase the filter effect in that
dimension. Filter (a) defines a low pass pyramid filter, (b) a high-pas filter in the range and
a low pass filter in the time domain. (c) define a low-pass filter in the range and a high pass
filter in the time domain. (d) defines a high pass filter in all domains named a Laplace
filter. b and c detects gradients while d detects second differentials.

a b c d
131 1 1 1 -1 0 1 0 -1 0
373 0 0 0 -1 0 1 -1 4 -1
131 -1 -1 -1 -1 0 1 0 -1 0
Figure 191. Four filters and their filter coefficients

Eq. 106 Q(m1 , m2 )   F (n1, n2 )H (m1  n1  1, m2  n2 )

n1 n2

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The equation demonstrates the convolution of a filter with an echogram. F holds the filter
coefficients as seen in Figure 191 while H is the echogram. Each sample with index m1
and m2 in the new echogram Q will be a sum of products between surrounding samples
from the original echogram and the filter coefficients.

FindObjects
Parameters: <Min> <Max>
Example: Load 0 1; FindObjects 5 55; show; DrawBorder 500; show; Free
Search trough TmpResultImage and locate regions. Each time the algorithm hits a sample
with echo intensity different from zero it will follow perimeter until it comes back to the
start point. All sample positions along the perimeter are noted in a list and the list is stored
as an object. Different lists are stored for every detected object and the numbers of samples
in each list indicates the perimeter length or size of the detected region. If the length of the
list or perimeter is shorter than min or longer than max it is deleted.

Find object can be applied as a separate command, but most commands needing it will call
it automatically.

FlatBottom
Parameters: <Option> <depth offset>
Example : Load 0 1; FlatBottom 2 0 OpenResultFile; Free;
Before running this command, it is important to ensure that a vertical bottom line has been
detected and that this line is correct. The command will use the bottom line when the new
flat bottom echogram is generated. First the average depth of the bottom line is found.
Then the range of the samples and the range of the single echo detections are corrected
according to the range of the bottom line. This will make a bottom related echogram with
the depth of the bottom at the average range of the bottom line plus the value of the depth
offset parameter. A new bottom line is also generated and stored with an additional Q in its
file extension.

The menu: Echogram=>Bottom=>Load or Save as can be applied to save and load the
bottom lines.

In addition to the new echogram and bottom file, a file with the same name as the
echogram, but with the extension .RangeCorr is written to the working folder. This file
contains the range corrections for each ping. The extension will have the same number of
Qs as the new corrected echogram file. The file is used to estimate the correct depth for the
macrophyte analysis implemented in January 2006. It may later be applied to find the
correct range in a range corrected echogram other places in the program where range is
important.

Warning:
When the Flatbottom command has been applied to generate a new echogram, depth or
range will not be displayed correct in the echogram caption and range bar. Tracking is
possible, but the range for the traced fish will not be correct. Biomass estimation can be
applied as long as the echogram is a 20logR echogram. If it is a 40logR echogram, range is
needed to find sv. With incorrect range the conversion from TS to Sv will be incorrect
resulting in erroneous abundance estimates. We may later apply the file .RangeCorr to

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include these operations.

Option:
2 Save the corrected echogram
3 Correct range for tracks in fish baskets
4 Do both 2 and 3
Free
Parameters: None
Example Load 0 1; Mean 1 3; show; Free
Ending a command series with Free will de-allocate memory reserved by the Load
command.

Fillgap
Parameters:None
An area in the amp echogram defined with intensity rising above the noise level may
interior gaps like a donut. The Command fills such gaps with intensity slightly above the
threshold. The command can be applied to avoid multiple single echo detections etc.

GetOriginal
Parameters: <What> <Q>
Example: Load 0 1; show; Segmentation 1 3 55 1 -6; show; Mean 3 3; show; SizeFilter 5
50 10000 1; GetOriginal D; show; Free;
Many of the image processes change the echo intensity in the Amp echogram. GetOriginal
restore the original values from the source file by reloading the file into the WorkImage.
Parameters:
<What>
 D= Reload only sample values into WorkImage where Workimage already have
samples above threshold. (D=Detected )
 N = Invers of the above option. (N=Not Detected)
 A = Reload all samples into the WorkImage.( A=All )

<Q>
This parameter is an integer and indicates the processing level measured in numbers of Qs
that the echogram to be loaded should have in the extension. As an example .uuu would be
the original level 0 while .uuuQ indicates processing level 1.

Grow
Parameters: <Min> <Max> <Size> <dir> <Melt>

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Example: Load 0 1; show; Segmentation 1 3 55 1 -6; show; Grow 20 500 1 Width Melt;
show; SizeFilter 5 50 10000 1; show; Free;
A detected region can grow by copying the samples along the regions border to the
surrounding areas. Only detected targets with perimeters within min and max will be
processed. Size defines how much the region should grow. Dir defines the direction of
growing. Dir can be Width, Height, Width+Height written in words like here. Melt
determines whether two targets are allowed to grow into each other and melt into one
region or not. Melt can have the values Melting or No melting.

HeaveCorrection
Parameters: <Filterwidth> <Amplify> <Option>
Example: Load 0 1; HeaveCorrection 21 1.0 0; show; free;
Example: Load 0 1; HeaveCorrection 21 1.0 4; OpenResultFile; show; free;

Depending on the option parameter, this command can correct range in the echogram as
well as in tracked fish stored in fish baskets. The first parameter is the number of bottom
detections to be averaged. The second parameter will be multiplied with the error estimate.
The third parameter is the option. Here 0 means test while 4 will force the command to
generate a new file with corrected range. The show command will display the result. The
OpenResultFile command will open the new file.

The command was implemented on request from Reiner Eckmann (Ge) in order to correct
for heave. If the transducer is moving up and down in the water due to waves, the distance
to bottom will change and reflect the waves. The HeaveCorrection command uses the
detected bottom and applies a mean filter. The result is a smoothed bottom line. By
subtracting the smoothed line from the original bottom line, a correction estimate is
obtained. This estimate is multiplied with the amplify parameter. The result is used to
move the samples in the Amp echogram, the single echo detections in the SED echogram
and the single echo detections in the fish baskets.

The FilterWidth parameter is the number of bottom detections to be averaged. E.g.

FilterWidth =21 will sum the 10 detections on each side of the ping in question plus the
detection at the ping in question and divide the sum by 21 to produce an average bottom
detection for that ping.

The Amplify parameter is a real factor which can be used to increase or invert the
correction effect. Normally Amplify =1.0 should be applied.

The Option parameter defines what the command will do.

Option=0: The command will plot the existing and the smoothed bottom line. No
changes will be made to the echogram or to any fish track. Zoom in at
different parts of the bottom and check that the smoothed line is behaving
as wanted.
Option=1: The command will show the corrected Amp echogram but nothing will be
stored. Press the enter key to see the original echogram again.
Option=2: A new corrected echogram file will be generated. The new file will have
the same name as the original file but with an additional letter Q in the
extension. Press Alt+0 to open a file with one .uuu in the extension. Press

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Alt+1 to open a file with .uuuQ, Press Alt+2 to open a file with .uuuQQ
and so on. See quick file open in the main file menu
Option=3: All tracked fish in all fish baskets will be corrected, but no correction will
be made to the echograms. One will see the change in the Amp echogram,
but this is temporary. Warning1! The correction will be carried out every
time the command is executed and multiple runs can cause erroneous
range correction.Warning2! Since only the tracks are corrected, it may
look like there are mismatch between the tracks range and the echoes in
the echogram when tracks are re-plotted in the echogram.
Option=4: This option combines option 2+3. If the resulting echogram is opened no
mismatch will be seen when tracked fish are re-presented in the echogram.

Figure 192. The Heave correction command estimates the heave by smoothing the bottom
line.

HitRemove
Parameters: <MaskName> [FitThreshold], [Threshold(dB)] [Replacement (dB) ]
[ReplaceAbove] [ReplaceBelow]
Example: Load Hitremove Mask2 90 -50 -70 0 0 ; Save 1 1 sv, Show; Free;

This is a morphologic filter that detects and replaces samples with the same pattern as the
mask. Not detected samples are left undisturbed. The mask is binary. A zero in the mask
refers to a value below the threshold in the echogram, while a 1 in the mask refer to a value
above the threshold. The example uses Mask2 defined below. It will remove all samples
that are standalone samples such as very short noise spikes from for example propeller
cavitation. A mask is said to be closed if it contain zeros around the border, and open if a
one is located on the border somewhere. See the mask examples below.
<MaskName>
Identify the mask defined in the mask window located below the command editor
[FitThreshold]
Default is 100% if the parameter is not applied. The algorithm count the number of
samples that fit the mask and calculate the percent fit in percent. If FitThreshold is set to
50% then half of the samples must fit the mask in order to be accepted as a fit.
[Threshold]
Only samples below the threshold are regarded equal to zeros in the mask. Thus the
threshold is important. If the command flow starts with Load 0 1, the echogram will be

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loaded down to the base threshold independent of the working threshold seen in the
echogram. If the load command is not followed by a 0 parameter, then the echogram is
loaded with the working threshold seen in the echogram. If the HitRemove commands
threshold parameter is applied, the threshold will be applied, but only if it is higher than the
loaded threshold. As an example, If the weakest echo loaded is -70dB, HitRemoves
threshold cannot force the weakest echo to be -80dB.
[Replacement]
If replacement is applied, the mask will replace the detected sample with the value given
for the replacement. If no replacement is applied, then detected samples will be given a
value below the base threshold. To apply a replacement value, Threshold must also be
applied.

[ReplaceAbove]
If a mask is open in the top, e.g. has one or more 1's along the mask top,,the given number
of samples will be replaced above each detected position.

[ReplaceBelow]
If a mask is open in the bottom, e.g. has one or more 1's along the mask bottom, the given
number of samples will be replaced below each detected position.

Example of masks
Mask1 and 2 below can be applied to remove spurious noise echoes such as propeller
capitation noise. Mask3 can remove unwanted vertical bars from for example an
interfering echo sounder or sonar. Mask1 is open in the corner, Mask2 is closed while
Mask3 is open in the top and bottom.

Mask1 Mask2 Mask3

10 000 010
00 010 010
000 010

Keep
Parameter [memory number]
This command allocate necessary memory and copies TmpResultImage to KeepImage for
later use. Keep can take a number parameter from 1 to 3 whitch referes to three different
memory locations. An echogram kept in memory 1 can be different from an echogram kept
in memory 2. If no parameter is given, then 1 is assumed.

Layer
Example: Load 0 1; Layer; show; Free;
This command removes every thing outside the layer defined in the echogram control
dialog at the layer bottom and noise page. It does the tricks independently of the layer
being displayed presented or not.

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Load
Parameter: [Threshold] [Erased]
Example: Load 0 1; Mean 3 3; Show;
The load command loads the open file into the TmpResultImage buffer. Every analysis has
to be started with the load command. The load command reallocate memory for
WorkImage and TmpResultImage.

The threshold and Erased parameters are optional and defaults to 0 1 if not applied.
However, if the last parameter is applied also the first must be applied.

[Threshold]
Threshold determines how the echogram shall be loaded into memory with respect to
threshold. The parameter is optional as indicated by the brackets. It is, however, needed if
the erased parameter is to be applied. The parameter can take two values 0 and 1
 Threshold = 0 will load all echoes above base threshold
 Threshold = 1 will load all echoes above the current working threshold.
[Erased]
The erased parameter determines how the commands will handle erased samples during the
processing. The Erased parameter is optional as indicated by the brackets. It can take three
values:
 Erased = 0 will handle all erased echoes as if they where thresholded
 Erased = 1* will handle all erased echoes as not erased.
 Erased = 2 will give all erased echoes the value closest to the base threshold.
* Default because most image analysis operators behaves best with this option.

Note that all erased samples in the input file will be seen as erased in the resulting output
file. The point with the erased parameter is only to control the internal image analysis
process. An example of the effect can be seen if we assume a line of samples with TS
values[-40, -40 -40] dB. If we filter these values with a mean filter we will produce an
output of 40 dB. However, if one of the samples is erased, then the filtered output will
depend on how we regard the erased sample.

LoadFreq
Parameter <number> [unit]
Example: Load 0 1; Keep 1; Loadfreq 38 kHz; save 11 11 Sv; Loadfreq 120 kHz; save 11
11 Sv;
The command look for a certain frequency or channel and load it into WorkImage if found.
Number can be either frequency such as 120 with unit being kHz, or it can be a channel
number like 3 with unit being ChNr. The command is useful for example if one want to
apply a mask made in one frequency to other frequencies. Open for example a 38 kHz
echogram and erase unwanted targets. Then the example command set above will create
two new files with the same processing level and where the same targets are erased in both
the 38 and 120 kHz. Echograms must have same filename except for the channel indicator
and they must have the same number of pings and samples. The system will warn if not.
Files with different number of samples and pings can be adjusted with the File => Merge
and resample dialog.

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LoadPhase
Parameter <Dimension>
Example: Load 0 1; LoadPhase ath; variation 3 1 -1023 -1 1; mean 3 3; Threshold_Lin 0
-40 ; show;
The command loads the sample angle data into memory. This enables image analyzer to
operate on the Alo and Ath phase echograms and to combine information from the Amp
and the phase echograms. Target detection power can be extracted from the variance in the
phase echogram and applied in the detection of a target in the amp echogram.

MaskEchogram
Parameter: < unit > <Item list >
Example1: Load 0 1 ; Mask kHz 70 120 200
Example2: Load 0 1 ; Mask Ch 2 3 4

The echogram loaded into the WorkImage will serve as the mask. A mask is an echogram
where samples have been erased. Samples below threshold will not serve as a mask. The
echograms listed in the item list will be loaded and samples marked as erased in the mask
will be erased in the loaded echograms. The item list can either contain channel numbers or
frequencies. The unit parameter determines whether the number in the list should be
interpreted as a channel number or a frequency. Only integer values are allowed in the item
list.

Input: In the example 1 and 2 the Load 0 1 command will load the last opened and active
echogram. This echogram is supposed to contain the mask in form of erased samples at
unwanted positions. If one echogram window is open, that echogram will be used as the
mask. If multiple echograms are opened, the last activated echogram will be loaded and
assumed to contain the mask.

Output: All echograms listed in the item list will be masked if found. Note that msk and
output echogram must differ.

A typical example of use is the removal of fish or noise in a multi frequency plankton
study. The echoes to be removed may be best observed in one frequency. For fish and
plankton that will probably be the lowest frequency. Noise from cavitations or from
another echo sounder may be best seen in other frequencies. The principle for masking is
that one erases the noise or fish in the echogram where it is easiest to see and then use that
echogram as a mask for the other frequencies. Start with the automatic target noise
separator and detect the noise automatically, then check the echogram and edit the result
with the manual erase / recall tools in case the automatic methods failed. When you are
satisfied with the result, use the prepared echogram as a mask to the other frequencies.

Technical details: Echosounders meant to work together in a multi frequency setup has the
same sample resolution and produce files with the same number of pings. In this case the
MaskEchogram command will do a sample to sample masking. When data comes from
different echo sounders not originally designed to work together in a multi frequency
setup, the mask algorithm will use range rather than sample numbers to do the masking. If

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the target has less or equal nr of ping than the mask echogram, the target will be fully
masked. If not, the algorithm will mask as much as possible.

Magnitude
Parameter: <TSdB>
Example: Load 0 1; Show; Filter b; Show; Keep; Filter c; Show; Magnitude 20; Show;
Free;
Calculates the magnitude of the gradients obtained with two high pass gradient filters
working in separate directions such as b and c described under the Filter command. To
avoid negative values the parameter TSdB lifts the result up from the base threshold.
Applying TSdB=0 results in thresholding of negative values. The example assumes that
filter b and c has been defined in similar way as described for the Filter command.

Mean
Parameters: <height> <width>
Mean low pass filter. Height controls the cut-off frequency in the range domain while
width controls the cut-off frequency in the time domain. The filter is a non edge preserving
convolution filter. Increased height and lowers the cut-off frequency.

Median
Parameters: <height> <with>
Median low pass filter. Height controls the cut-off frequency in the range domain while
controls the cut-off frequency in the time domain. The filter is a edge preserving algorithm
based filer.

MFClass2Freq
Parameters: <Rule nr.>, <noise gap>
The commands produce a mask based on the relationship between the intensity of the
samples in the involved echograms. Initially the mask is set to zero for all samples. The
rules are applied to individual samples as follows
1. > If A > (B + NG ) then Mask=1
2. < If A < (B – NG ) then Mask=1
3. = If A > (B – NG ) and A < (B +NG) then Mask=1
4. ≠ If A < (B + NG ) and A > (B-NG ) then Mask=1

Where the number indicates the rule number, NG = noise gap. A, and B are different
echograms. The created Mask will be available in the WorkImage after the call.

MFClass3Freq
Parameters: <Rule nr.>, <noise gap>
The commands produce a mask based on the relationship between the intensity of the
samples in the involved echograms.

Initially the mask =0 for all samples. The rules are applied to individual samples as follows
1. > > if (A > B+NG) and (B > C+NG) then Mask = 1
2. < < if (A < B- NG) and (B < C-NG) then Mask = 1
3. > < if (A > B+NG) and (B < C-NG) then Mask = 1

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4. < > if (A < B- NG) and (B > C+NG) then Mask = 1

5. = = if (A < B+NG) and (A > B-NG) and (B < C+NG) and (B > C-NG) then
Mask= 1
6. ≠ ≠ if (A > B+NG) or (A < B-NG) and (B > C+NG) or (B < C-NG) then
Mask= 1

Where the number indicates the rule number, NG = noise gap. A, B and C are different
echograms. The created Mask will be available in the WorkImage after the call.

NewSEDechogram
Parameters: <MinValue>, [Destination], [Phase_file_location]
Example: Load 0 1; show; Segmentation 1 3 55 1 -6; show; Mean 3 5; show; SizeFilter 5
50 10000 1; show; NewSEDEchogram 0; Free;

The command generates a new echogram from detected regions in the Amp echogram. For
each ping detected regions are analyzed with a single echo detector given strict criteria.
If an echo is accepted, angular positions are extracted from all angle samples with the same
index as the samples covered by the detected echo intensity. The echo is marked as a high
quality echo. If not, a peak detector is applied and the angles are obtained from the phase
file at the index of the peak sample. The echo is marked as a low quality echo. Only echoes
above the min value will be applied in the new file. The value 0 will result in the lowest
possible threshold. This is recommended. Destination is the folder where the resulting file
should be placed. Phase file location indicates where the file containing the angle samples
should be located. A phase file is needed. The file has the same name as the echogram file
but the extension .Phase. Phase files are generated during the conversion if the original
files contain sample data and if the extract phase file is checked at the converters first page.

Next
Example: Load 0 1; mean 1 3; Show; Next; Free;
If more than one file has been selected in the file open menu, the first file is opened and the
others are noted in the internal quick file change list. This command will close the open
file and open the next. Then it will restart the processing of the image analysis from the
first command.

PassiveNoise
The PassiveNoise command removes passive noise from an echogram. It can either be
told about the noise to remove or it can detect the noise itself before removing it.
To prevent the system from detecting the noise and to use the applied default noise value,
simply write the word UseDefault as the 4th or 5th parameter.

Detecting passive noise in an active recording:

To detect passive noise, the algorithm search for a range where the returned energy is at a
minimum. In many cases this energy level will be close to the passive noise level. Prior to
this command one should apply a running mean filter operator such as "mean 11, 11 Lin".
The “PassiveNoise” command will then look for minimum value in the filtered echogram
and not in the individual samples in the original echogram.

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Input and output

The algorithm will use the “WorkImage” containing the result from the previous command
to search for the noise levels. It will use the echogram stored in the keep1Image as source
when it subtract the noise. The final noise corrected echogram will be found in the
“WorkImage” when the command has finished.

WorkImage[ I , j ] = Keep1Image[ i , j ] - MinIntensity(WorkImage[ i ])

This is a quasi-formula. Index i and j are ping and sample number respectively. The
subtraction is carried out in the linear domain with TVG removed. WorkImage is brought
back to logarithmic domain with TVG added.

Parameters:
1. Start Range: The algorithm starts searching for passive noise from this range.
StartRange=-1 will force the algorithm to start to search from the closest available
distance from the transducer.

2. Stop Range: The algorithm stop searching for passive noise at this range.
StopRange=-1 will force the algorithm to search to the maximum range in each
ping.

MaxNoise and DefaultNoise parameters

3. MaxNoise : If the detected noise exceed the value of this parameter, the detected
noise is considered not valid and the algorithm will take the noise found in an
earlier ping.

4. DefaultNoise: If no passive noise has been detected yet, then the value of this
parameter will be applied.

Since noise can be both additive and subtractive, searching for noise on individual samples
will return unnatural low results. Some pings may be influenced by strong noise so that the
found minimum will be higher than the passive noise. Two parameters are applied to avoid
this problem, MaxNoise (dB) and
DefaultNoise(dB). MaxNoise is a threshold value. If the lowest detected energy level is
higher than this MaxNoise value in a particular ping, the system will use the last found
noise level instead. If no noise level yet has been found below the MaxNoise threshold,
then the system will use the value specified by the DefaultNoise parameter. To find these
two parameters one can use the oscilloscope (Menu: Analysis=>Data
insight=>Oscilloscope.)
We Here turn of the TVG checkbox and find a place in the echograms with very low
reverberation level. Use the Oscilloscope in mean mode (select mode from the
oscilloscopes right mouse button pop up menu) and draw a rectangle around the selected
low noise region. This will give good candidates for the MaxNoise and DefaultNoise
parameters.

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5. ShowRange : This parameter is optional and only applied for test. The range where
the passive noise is detected will be “painted” with the dB color given. E.G if the
color bar show that red = -35dB, then setting ShowRange to -35 will paint the
detected range with red color. The parameter is optional and should only be used
for testing.

6. ShowNoise: Typing this word after the ShowRange parameter will produce an
echogram consisting of the detected noise including the marks from the
ShowRange test. The parameter is optional and should only be used for testing.

7.

An example for test is

Load
Keep
mean 5 45 lin
PassiveNoise -1 -1 -130, -130 -35
Show
Free

An example that produces a new echogram is this

;***********************
; Look for and remove Passive noise
; in active recorded files.
;**********************
load
Keep ; Save the source for the Passive noise command
mean 5 5 lin ; Filter the noise before studying it.
PassiveNoise -1 -1 -130 -130 ; Use detected noise if it is below -130 dB If above and
not found earlier, use -130.
show ; Present the result
save 1 0 Sv ; save the corrected amp echogram and Uncorrected
SED.
Next
Free

OpenResultFile
If a set of commands involves a command producing a new file, this command will open
the produced file. The command is naturally placed as the last command in the processing
series. Example: Load 0 1; mean 5 5; Save; OpenResultFile

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Pause
Example: Load 0; mean 1 3; Show; Pause; Next; Free;
Stops the execution temporarily. Pressing the analysis button will start processing of the
remaining commands. Useful when testing series of commands.

PeakDetection
Example: Load 0 1; Show; Segmentation 1 3 55 1 -6; show; PeakDetection; show; Free;
Detect peak values in regions detected by other methods such as thresholding,
segmentation SED etc.

RemoveDetection
Example: Load 0 1; Segmentation 1 3 55 1 -6; SizeFilter 5 75 100000 1; Keep; reLoad 0 1;
RemoveDetection; show; save 1 1
This command has been designed to remove fish from plankton studies, but it can be used
to remove all kinds of detectable targets. The principle is that one first runs what is needed
to detect the targets to be removed, call the keep command, loads the original echogram
and then calls the RemoveDetection command. The data in the keep image will then work
as a mask for the original echogram, removing all echoes at positions where something is
found in the keep image. Ending with the command save 1 1 saves the resulting Amp
echogram. The SED echogram will be saved at locations where the resulting Amp
echogram has echo intensities above the threshold.
As an alternative, skipping the RemoveDetection and apply the Save 5 3 command will
result in a new file where detected targets has been erased but not removed. This is a more
correct method if one want to withdraw targets from Biomass estimation. See the save
command.
Save
Parameters <Amp option> <SED-option> <Echogram type> [filename]
Echogram type can be TS or Sv written like here.
If a filename is given, then the echogram will be saved to that filename. If no filename is
given the file will be saved with the same name as the loaded filename or echogram but
with an additional Q in the extension to indicate a higher processing level.
Amp and SED options can be numbers from 0 to 18 with the following meaning

0 save Orgiginal
1 save WorkImage
2 save Keep1Image

3 if Keep1Image <> 0 save Original else save threshold

4 if Keep1Image = 0 save Original else save threshold
5 if WorkImage <> 0 save original else save threshold
6 if WorkImage = 0 save original else save threshold

7 If Keep1Imag <> 0 save WorkImage else save threshold

8 If Keep1Imag = 0 save WorkImage else save threshold
9 If WorkImage <> 0 save Keep1Image else save threshold
10 If WorkImage = 0 save Keep1Image else save threshold

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11 if keep1Image <> 0 Save Erased Original else Save original

12 if keep1Image = 0 save Erased Original else Save original
13 if WorkImage <> 0 save Erased Original else Save original
14 if WorkImage = 0 save Erased Original else Save original

15 if Keep1Image <> 0 save Erased WorkImage else save WorkImage

16 if Keep1Image = 0 save Erased WorkImage else save WorkImage
17 if WorkImage <> 0 save Erased Keep1Image else save Keep1Image
18 if WorkImage = 0 save Erased Keep1Image else save Keep1Image

Original means the original echogram without any modifications. The other image names
refer to the images listed in Table 12. They may have been modified by other commands.
The images are handled sample by sample while the SED echogram is handled echo by
echo.

Example: save 1 0 sv will save the echogram with the amp echogram as an Sv echogram
comming from the WorkImage and the SED Echogram being the original SED echogram.
SED echgrams are always 40 log R echograms.

SED_Save
Parameters: <Min.Value> <Min.EchoLength> <Max.EchoLength> <Max.GainComp.>
<Max.PhaseDev> <PulseLevel> <Multiple Peaks> <Plot>
Example: Load 0 1; show; Mean 1 3; show; SED_Save -50 0.6 1.8 3 1.2 6 2 0; show; Free;

This command calls a traditional parameter based single echo detector. PulseLevel defines
the level in dB where the echo length is measured relative to the peak.

See the section Single echo detection in chapter 4 for more information about single echo
detection and single echo detector parameters.

MultiplePeaks can be 0, 1, or 2 where 0=Off, 1=medium, 2=strong. Parameter value 1

slices the echo pulse into 1.5dB levels. If the rising and falling intensity crosses one of the
levels four or more times, the echo is discarded. Parameter value 2 counts all peaks
independently of the size of the peaks. Echoes with more than one peak is discarded.

Plot=0 will detect all the samples while plot=1 will detect only the peak values. The result
will be saved in a new file marked with a Q in the extension. Echoes within the high
quality definition will be marked as high quality echoes.

SED_Test
Example: Load 0 1; show; Mean 1 3; show; SED_Test -50 0.6 1.8 3 1.2 6 2 0; show; Free;
Same as SED_Save except that no echogram will be saved.

Segmentation
Parameters: <F-height> <F-width> <B-height > <B-width> <SNR>
Example: Load 0 1; show; Segmentation 1 3 55 1 -6; show; Free;

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This command is the most important command forming the Crossfilter detector. F-height,
F-width defines the cut-off frequencies in the foreground filter while the B-height, B-width
defines the cut-off frequencies in the filter detecting the background intensity. SNR defines
the difference between foreground and background echo intensity for the foreground to be
detected as a signal.

SetSampleValue
Parameter: <dB>
Example: Load 0 1; keep; mean 55 1; threshold 0 -45; mean 5 5; show; SetSampleValue
-0; show; ThresholdAdd -12; show; keep; reload; save 3 1;
Sets all samples with values above the base threshold to the value described by the
parameter. The command can be used to define a mask as in the example. Here schools and
bottom are masked and a new echogram without the fish schools and bottom is produced.
Show
Displays the contents in the TmpResultImage in the echogram window independently of
the echograms display mode. The presentation is not permanent and the echogram update
will bring the echogram back to normal. To see a processed result permanent, the result has
to be saved to a new file and opened. The save command can do this.

SizeFilter
Parameters: <Min> <Max><Break><Size type>
Example: Load 0 1; Segmentation 1 3 55 1 -6; show; SizeFilter 5 20 10000 1; show Free;

When targets have been detected the size filter can be applied to remove small and large
targets. The filter accepts only targets greater than the minimum value and smaller than the
maximum value. Testing targets size will break at the break value. Size type can be one of
the following:

Size Name Comment

type
0 Perimeter The sum of samples found by “walking” around the border where
length the detected target intensity exceeds the threshold.
1 Track length Measured in number of pings
2 Mean echo Mean echo length measured relative to the transmitted pulse.
length
3 Max echo Max height of a track measured relative to the transmitted pulse.
length
4 Area The area of a track is the number of samples that builds up the
target.
5 Ratio Ratio between track length and mean echo length.
High ratio values indicates thin and long tracks such as echoes
from a stone on the bottom in a fixed location river recording.
Medium values may indicate passing fish while small values may
indicate fish schools, boat wakes, sea lions etc.
6 Mean TS dB Mean TS of all samples in detections. Independent of whether the
echogram contains Sv or TS values they will be converted into
40log sigma and averaged. The average is converted back to TS

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before comparing with the Min and max parameters. Note that it
is the uncompensated TS that is handled here and that the TS
values will be influenced by earlier commands in the image
analysis process such as filters. Exact filtering on compensated
TS can be applied later by setting track filters in the fish baskets.
7 Max TS dB Max TS of all samples in detections. See comments for Mean TS
dB
8 Std. dev Alo Std. dev of the along ship angles. If max is set to 1.2 targets with
std.dev > 1.2 in the along ship direction will be removed.
9 Std. dev Ath Same as above but for the Athwart ship angles.

ThresholdAdd
ThresholdAdd
Parameter: <offset (dB)>
Load 0 1; show; mean 3 3; Show; keep; Mean 21 21; Show; ThresholdAdd -6; Show;
Free;
Uses the echogram stored in KeepIm as a threshold for the InIm to produce the OutIm
echogram. Offset is added to each sample in the KeepIm echogram and the result is
compared with the intensity in the corresponding sample in InIm. the sample in InIm is
greater than the sample in KeepIm, that sample in InIm is copied to the corresponding
sample in OutIm. If not Outim is set to zero.

If (keepIm  offset)  InIm

Eq. 107 then OutIm  InIm
else OutIm  0
Switch
Parameters: [a b]
Example: Load 0 1; Mean 3 3; show; switch 1 2; show; free; After the switch command,
show will present the TmpResultImage instead of the WorkImage. The numbers a and b
relates to the images listed in Table 12. If no parameters are given , Switch 1 2 will be
assumed.

ThresholdLin
Parameters: <a> <b (dB)>
Example: Load 0 1; Show; Threshold 5 -40; Show; Free;
Results in a thresholded echogram.

Threshold  a  Range  b

ThresholdReg
Parameters;<OffsetdB><MinR> <MaxR>
Example: Load 0 1; show; ThresholdReg -45 10 25; Show
For each ping, linear regression is applied to obtain the parameter a and b. Only samples
between minR and maxR are applied. This make it possible to avoid influnece from
transducer ringing and bottom. The offset is added the parameter b. The resulting
(ax+b+offset line is applied as a threshold. Values below the threshold is set to Zero in the

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TmpResultImage.

Threshold  a  Range  b  offset

Tracking
Parameter: <draw>
Example: Load 0 1; show; Segmentation 1 3 55 1 -6; show; Mean 3 5; show; SizeFilter 5
50 10000 1; show; tracking; Free;

This command utilizes SED-tracking guided by image analysis. Only regions in the in the
Amp echogram seen with echo intensity rising above the background threshold will be
tracked. First the command obtain the perimeter from all clusters of samples (coherent
samples rising above the defined base threshold) in the Amp echogram. The perimeters
serve the same function as the box the operator draw around a set of echoes with the mouse
when echoes are tracked manually. Only SED-echoes within each box will be combined.
How they will be combined depends on how the Tracker windows SED page has been
adjusted. As an example, if auto tracking has been selected, the auto-tracking parameters
will be involved. If manual tracking has been selected, all echoes within each detected
region in the Amp echogram will be combined into a track.

The draw parameter was implemented mainly for test purpose. If applied, the pixels along
each detected perimeter will be set to a fixed TS-value. To see the perimeters, the tracking
command must be followed by a Show command. It may also be necessary to zoom the
echogram in on a few tracks when using this option.

See also the description of the Crossfilter tracker template in the section Crossfilter
tracking in chapter 19. This template set up the commands for a Crossfilter detector
followed by the Tracking command.

ZeroToOne
Load 0 1; Segmentation 1 3 55 1 -6; show; ZeroToOne; show; Free;
Lift the echograms echo intensity 0.1 dB up from the base threshold.

Commands under test. Do not try these commands

Do not complain if the computer crash or the sonar files are damaged when trying the
commands!
Balance <Factor> <Offset (dB)>
HitAdd <MaskName>
HideSED. Crash the system
Shrink <MinPerimeter> <MaxPerimeter> <size> <color>
Simulate
Subtract2 <TSdB>
Qtracking Min Max

Variance
Parameter<hight> <width> <factor1> <factor2>

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Example Load 0 1, LoadPhase Alo, Variance 3 3 300 0.3 Save 1 0, OpenResultFile

The command converts echo regions with low variance into high intensity and vice versa.
Height is the number of samples and with the number of pings involved in the variance
calculation. Factor 1 is subtracted and factor 2 is multiplied with the resulting variance for
each sample. This is needed to produce an intensity that can be displayed within the
selected dB scale, e.g from -100..-10 dB

Template dialogs
Template dialogs assists in setting up and running the image analysis. Most templates are
located in the main menu Analysis = Pre-analysis. Templates for bottom detection. Single
echo detections, filtering and tracking are available here. The templates generate a rather
fixed series of commands found to work well in many cases. However, the operator is free
to edit the resulting commands by adding, deleting or re-ordering them.

Filter template

Figure 193. The filter template dialog is accessed from the main menu: Analysis - Pre
analysis menu.
Aim
The dialog can smooth echograms. This can be useful for noise reduction and for ease
studying targets.
Test button
Process only the visible part of the echogram. The result is displayed in the echogram, but
not stored on disk. The original unfiltered echogram will reappear as soon as the echogram
view will disappear at once, but nothing is stored to and the result cannot be tracked. The
aim is to test various parameter settings in a fast way.

Run button
Generates a job, which will produce a new file. The new file is marked with a letter Q in
the extension. Pressing the short key Alt+Q can open the file. (It can of course, also be
opened from one of the file open dialogs)

Pressing the Run Job button will write the following commands to the Tracer windows
image page. Load 0 1; Mean 1 3; Save; Show; Selecting a median filter will generate the
commands Load 0 1; Median 1 3; Save; show;

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Stop button
This button is only visible during execution. Pressing the Stop button will halt the
execution at the first possible point.

Generate commands checkbox

If checked, commands will be written to the Tracer windows command editor but
execution will not take place. The caption of the Run and Test buttons will change to
indicate this.
The checkbox enables the commands to be further edited before execution.

Process all selected files checkbox

If checked all selected files will be processed when the run button is pressed.

Open result file checkbox

If checked the last file processed by the Run button will be opened. Alternatively, press the
short key Alt+Q or use one of the file open dialogs to open a result file. Result files has the
same name as the original file but a letter Q is added to the extension each time file is
processed.

Filter width
Filter width determines the cut-off frequency in the time or ping domain. Increase the
value to lower the cut-off frequency. A number 1 will not give any filter effect at all.
Higher numbers will give visible results. Use odd numbers.

Filter height
Filter height determines the cut-off frequency in the range domain. Increase the value to
lower the cut-off frequency. A number 1 will not give any filter effect at all. A number 55
will remove most frequency components and leave only the low frequent background
intensity variations.

Bottom detector template

The Bottom detector is accessed from Sonar5s main menu: Analysis - Pre analysis. It is
described in chapter 4s section: Bottom detection

Masking template
The masking template is accessed from Sonar5s Sonar5s main menu: Analysis - Pre
analysis-> noise menu.

Single echo detection template

The Single echo detector template is accessed from Sonar5s main menu: Analysis - Pre
analysis. It is described in chapter 20. See also the section Single echo detection in chapter
4 for information abut single echo detection in general.

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Crossfilter detector template

The Crossfilter template is accessed from Sonar5s main menu: Analysis - Pre analysis.
The Crossfilter detector is described in chapter 19

Crossfilter tracker template

This tracker template is accessed from Sonar5s Analysis menu: Analysis = 1-Set up=
Tracking=Crossfilter, described in the section: Crossfilter tracking found in chapter 19.

Passive noise subtraction template

This template is designed to set up a command series for removing passive noise. Details
for the following methods and parameters are described in the section describing the
PassiveNoise
Command executed by this template.
Method panel
This panel has two options, Dynamic noise and Constant noise. Select Dynamic Noise to
let the system automatically detect and remove passive noise in the echograms. The
method searches within the applied range for a minimum echo level and assume that this
level is about the same as the passive noise. Select Constant noise to subtract a constant
noise level. The noise level can be found from a passive file by pressing the button to the
right in the template named “Study noise” button.

When the Dynamic noise method is selected, the following parameters will appear
Noise panel with the parameters Max Noise, Default noise and Offset
Search range panel with start range and stop range parameters
Filter dimension panel with filter with and filter height parameters.
Options for the test button panel. Settings in this panel do only work when the Test button
is used. The mark detected range with xx color will draw a line at the range found to
contain passive noise detected by the automatic noise detector. The xx should be set to a
dB value according to the echogram color scale, and it will then mark the detected line
with that color.

Echogram enhancement with low pass filters

Echogram with low signal to noise ratio (SNR) can be difficult to interpret. Applying a
filter might help.

There are two main kinds of low-pass filters, the edge preserving and the non-edge
preserving. The mean filter is a typical non-edge-preserving filter, while the median is a
typical edge-preserving filter. Both can be applied to improve fish tracks while non-edge
preserving filters should be applied when the aim is to detect the background reverberation
noise level.

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If the fish tracks are relatively stable in range, a long, thin filter might improve the fish
track substantially. Try a mean or median filter with the dimension 1x3, 3x5, 3x7 or 3x9. If
a fish track is not stable in range, more squared filter dimensions might be better suited like
3x3, 5x5 and so on.

To detect the background reverberation level high thin or large filters might do, like 55x1
55x5 or 19x19.

Example 3: A filter command may look like this:

Load 0 1 ; Load the file into memory
mean 3 7 ; filter the echogram
save test ; Save the result to a new file with the name test.uuu
show ; show the results

Single fish detection in noisy environments

Traditional single echo detectors optimized for accurate TS calculations may not work well
in noisy environments. Echoes from fish will frequently be rejected while fluctuations in
the background will be detected as fish echoes. This will result in fractionated tracks
surrounded with noise. Hence, automatic tracking of SED-echoes will not work well. To
solve this one can (a) improve the SED echogram by applying the Crossfilter detector
before starting the tracker or (b) apply the Crossfilter tracker.

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Main menu

This window can study echo intensity and frequency distributions in time and range.

ABOUT ...................................................................................................................................................................370
Data input from the echogram .........................................................................................................................370
TS VARIATIONS IN TRACKS ....................................................................................................................................370
TS VERSUS FISH ASPECT ........................................................................................................................................371
SWIMMING MOVEMENT AND TS ............................................................................................................................371
ECHO SIGNATURE ..................................................................................................................................................371
ECHO INTENSITY AS A FUNCTION OF RANGE ..........................................................................................................372
THE POPUP MENU ...................................................................................................................................................372
Help menu ........................................................................................................................................................372
Show commander menu....................................................................................................................................372
Mode menu .......................................................................................................................................................372
Title ..................................................................................................................................................................373
Disconnect........................................................................................................................................................373
Copy to clip board => Copy window to clip board .........................................................................................340
Copy to clip board => Copy data to clip board ..............................................................................................340
Changing between logarithmic and arithmetic mean menu .............................................................................340
Fourier analysis menu .....................................................................................................................................341
Playing ping on sound card menu ....................................................................................................................341
Noise analysis ..................................................................................................................................................341
EXPORTING DATA TO OTHER PROGRAMS ...............................................................................................................341
See Examples....................................................................................................................................................342
CHANGING AXIS, TITLE, FONTS, COLORS ETC. ........................................................................................................342
THE FOUR MODES OF OPERATION ...........................................................................................................................342
Ping mode ........................................................................................................................................................343
Mean ping mode ...............................................................................................................................................344
Peak mode ........................................................................................................................................................344
Time mode ........................................................................................................................................................344
Size distribution mode ......................................................................................................................................345
Examples ..........................................................................................................................................................345
PLAY THE ECHO ON THE SOUND CARD ...................................................................................................................327

Figure 194. Oscilloscope window displaying data for one ping within a layer.

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About
The oscilloscope window can be applied to study the shape of echoes, evaluate bottom
substrates, study the TS stability of targets, extract echo intensity from experiments such as
fish mounted in a in merry go round. Fish swimming movement can be studied and Fourier
analysis are available.

The oscilloscope window displays the echo values obtained in the Amp echogram. Hence,
the Amp echogram must be available in the sonar file. The oscilloscope window has four
modes. Ping, mean, peak and time.

Ping and mean modes study the echo intensities as a function of range. In peak mode, a
peak detector is activated. This detector detects and presents the peak in each ping. In
combinations with the Echogram window's rectangle and layer functions this is a powerful
tool. Time mode displays the echo intensity from the range bin pointed at with the mouse.

In addition a Fourier analyzer has been implemented. This was originally implemented to
test whether it was possible to detect swimming pattern from fish tracks. It can be useful
for other kinds of studies such as frequency studies assisting tuning of noise filters etc.

Data input from the echogram

Data to be displayed in the oscilloscope window are selected in the echogram window. In
ping and time mode the oscilloscope reflects the ping or range bin pointed at by the mouse.
In the other modes a region has to be selected in the echogram.

a) by drawing a rectangle around some interesting echoes with the mouse,

b) by defining a layer and starting a layer analyze.

The range viewed by the oscilloscope can be zoomed in two different ways.
a) Defining a layer in the echogram window.
b) Zooming the echogram window.

More than one oscilloscope window can be opened at the same time. Echo information
from different regions and different files can be compared. The disconnect-function must
be activated to prevent an oscilloscope from changing when another oscilloscope window
is updated. With many oscilloscopes on the screen, the title function can be helpful.

TS variations in tracks
To study intensity variations in a track, set the oscilloscope in peak mode and draw a
rectangle around the track in the echogram window. The echogram automatically sends the
echoes within the rectangle to the oscilloscope's peak detector, which will plot the peak
values versus time.

To see the details of the detections, the copy to clip board menu must be selected. This
produces a table containing ping no., echo intensity and range. for each of the detections.
Paste the table into a spreadsheet like Excel in order to see the table.

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Hint! The peak detector detects peaks and does not follow tracks. If there are disturbing
echoes near by, these can be erased temporarily. (See the section "Erase unwanted echoes"
in chapter 6)

TS versus fish aspect

Fish in a marry-go-round experiment reveals the TS versus fish aspect. A fish in a carousel
produces a long thin line with varying intensity in the echogram.

When the fish approaches the head and tail aspect it is often difficult to get reliable single
echo detections from the fish. Hence, analyzing the amplitude information can provide a
better way. With the fish mounted on the acoustic axis, the echo intensity will be the same
as found in the single echo detections.

Open the echogram control dialog from the echogram menu and select the page marked
layer bottom and noise. Here turn on pelagic layer and trim the layer lines to contain as
little as possible from the surroundings. If this is not possible because the echoes are
moving in range, a bottom layer can be used. When the layer is placed correct, check the
bind to layer checkbox.

Open the control dialogs analyze page and press the pelagic layer button, then the All file
button and after that the analyze button. This will display TS as a function of ping in the
layer. The aspect is found from the variations or from notes about the marry go round'
position as a function of time.

To see the details of the detections, the copy to clip board menu must be selected. This
produces a table containing ping number, echo intensity and range etc. for each of the
detections. Paste the table into a program like Excel in order to see the table.

It may also be of interest to study the frequency spectra in the fish echoes to check for side
lobes in the reflections from the fish etc. See example 2

Swimming movement and TS

The peak detector can be used to study TS versus fish swimming movement. See TS
variations in tracks. Selecting Fourier analysis from the popup-menu after the track has
been detected plots the frequency spectra of the TS variation.

Echo signature
There are many cases where the echo signature is of interest. Examples are studies of
bottom substrate, Fish detection near the bottom and signature from different fish species
and targets.

With the Oscilloscope in ping mode, pointing the mouse at a ping plots the echo intensity
versus range in the oscilloscope. To focus on special events, define a layer in the echogram
or zoom the echogram in on the event.

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Echo intensity as a function of range

With the Oscilloscope in ping mode, pointing the mouse at a ping plots the echo intensity
versus range. To focus on special events, define a layer in the echogram window.
Use the Fourier analysis to study the frequency spectra in the range domain.

The popup menu

Figure 195. Pressing the right mouse button while pointing at the oscilloscope window
opens the popup menu.

Help menu
Presents this chapter

Show commander menu

Show or hide the top commander. See the section: Charts, in chapter 2 for a general
description of the chart and the commander.

Mode menu

Figure 196. The mode menu presents the four available modes and their short keys.
In general pressing the Shift key is the simplest way to change mode when the oscilloscope
window is active. The Shift key toggles the modes in all Sonar5's windows and the name

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shift indicates a change. Hence, it is easy to remember. The Shift key is larger than most of
the other keys and easy to hit.

Title
Asks for a title to be added to the chart

Disconnect
Prevent the oscilloscope from receiving more data from the system. Apply this when
different oscilloscopes are applied to compare the signals from different places in the
echogram.

Copy to clip board => Copy window to clip board

Copies the graph as a picture to the clip board from where it can be pasted into programs
like Word or Excel .

Copy to clip board => Copy data to clip board

Copy data to clip board. The data tables transferred to clip board will depend on the
oscilloscope mode. The data is separated with tabulator characters which works well when
pasted into programs like Word, Excel, Statgraphic etc.

Changing between logarithmic and arithmetic mean menu

Opens the system configuration dialog at the page controlling this option

Fourier analysis menu

Displays the frequency spectra of the ping in ping and mean mode. Displays the frequency
spectra of a fish track etc in peak mode.

Figure 197. Time domain frequency spectre with (upper) and without (lower) a fish in the
beam. Note the concentration of energy in the lower spectra when a fish is in the beam.

Playing ping on sound card menu

This menu enables the pings to be played on the sound card when the oscilloscope window
is in range mode. The echograms layer, bottom line and zoom functions can limit the range
to be played. Pointing with the mouse at a ping in the echogram plays that ping.

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Noise analysis
Layer mean versus range
This menu item opens an additional panel where one can define a layer. Then this layer
will be placed at an indicated start range and the mean Sv will be estimated. The layer is
moved one layer thickness down and the next mean Sv will be found. In the end all the
mean Sv values are plotted as a function of range
Detection range

Figure 198. The oscilloscope windows range detection tool box panel.
In a multi frequency survey it is important to know the detection range or the range where
a target of certain size disappear in noise. The method assumes that a passive recorded file
is presented in the echogram. Selecting the detection range menu add a toolbox panel to the
Oscilloscope window. Type the size of the wanted targets and a noise gap into this panel.
10 dB is often applied in such estimations. Select a region in the echogram with the mouse
or by typing the ping range limits in the panel and then press the Go button. The
oscilloscope will plot range against the off axis angle where the target will disappear. This
angle decline with increasing range until it eventually hit the R-axis. At higher range or at
angles outside the function, that target can’t be detected.

Passive noise

Figure 199 The oscilloscope windows passive noise toolbox panel.

Right click in the oscilloscope and select noise => passive noise to see this panel. The
panel is designed to help studying passive noise. Passive noise can be found from passive

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recorded file and at special places in active recorded files. Robertis and Higginbottom,
(2007) gives a brief review of publications dealing with passive noise found in active and
passive files and present a method for detecting passive noise in active files. A variant of
this method is implemented in Sonar5-Pro’s passive noise subtraction tools.
Passive noise comes from various electronic phenomena in the echosounder
electronics, from other electronic equipment, from molecule movements in the waters and
from external sources like other echo sounders, propeller noise and animals. When we
record an echogram we do not see Sv or TS but (Sv+NL) or (TS+NL) where NL is the
Passive noise level. Normally NL is much lower than Sv or TS and can be ignored.
However, for higher frequencies in multi-frequency recordings and in situations where one
want to push the limits with respect to target size and range, noise removal can be
important.

Modes
The oscilloscope window has many different modes found by right clicking with the
mouse in the oscilloscope window and selecting Display modes in the appearing popup
menu. The two first modes are the same as the modes seen in the Passive noise panel. If a
different mode is selected in the popup menu, the Passive noise panel will disappear. The
mode selector in the Passive Noise panel is placed there for convenience and provides the
following options.

Pointing mode: Point at a place in the echogram to see the noise level index at this place.
The values in the filter dimension panel will be used for the filtering to find the mean
noise. With large values one may feel that the system works slow when moving the mouse
in the echogram.

Rectangle mode: Draw a rectangle in the echogram to see the noise level index within the
rectangle. The filter size will be set to match the selected region in the echogram before the
Noise level index is estimated.

Apply button
This button transfers the settings in the Passive Noise panel to the Passive Noise
subtraction dialog whether it is opened or not.

Subtract Button
This button opens the Passive Noise subtraction dialog. This dialog has various tools for
subtracting noise from echograms. The Passive Noise subtraction dialog can also be
opened from the Main menu: Analysis=>Pre-analysis=>Noise

Noise Level Index

It is possible to estimate the true noise level defined as the Noise intensity in dB relative to
reference intensity, but this would require that the operator apply more parameters such as
the internal resistance of the transducer. In order not to burden the operators with more
parameters than necessary we detect a Noise level index instead. This index can be used
directly for noise correction and for comparing different equipment and installations. The
noise level index is estimated in the following way:

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NLI  TSuM  TL( R )

or
NLI  Sv M  TL( R )  Vp ( R )

Where TL is the transmission loss and Vp the pulse volume. In this way the reported NLI
will be the same independent of range and independent of whether the echogram presents
the data as interpreted as Sv or TSu.

When a running mean filter with dimensions greater than 1x1 is applied, the reported NLI
will be estimated in the linear domain and the result converted back to the logarithmic
domain.

N 1
1
NLI  10 log
N
10
i 0
NLI / 10

Where N is the number of involved samples defined by the running mean window.
To see the NLI in the oscilloscope chart, check on Remove TVG boxes in the top panel.

Exporting data to other programs

The copy to clip board menu choice exports data
Data can be exported from the oscilloscope window. This is done trough Window's clip
board function. The complete oscilloscope chart can be exported or printed as a bit-map
and the echo data can be exported as tables. Tabulator characters separates columns in
these tables and makes them suited for pasting to programs like Microsoft's Word and
Excel.

The chart is copied to clip board by clicking the copy button at the windows top panel.
Numerical tables are copied by the right mouse button's popup menu or by pressing the
Ctrl-C key. The type of data copied in this way will depend on the oscilloscope mode. In
peak mode the Ctrl-C key will produce a table containing ping number, peak value and
range. In the popup menu the user can select whether survey information and SED
information shall be added to the table or not.

See Examples
Example 4: Extract the mean peak-value from a target and Example 5: Extract the intensity
along a target in peak mode.

Changing axis, title, fonts, colors etc.

Pressing the top panels edit button can change all features of the oscilloscope window.

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The four modes of operation

Four modes are available;- ping, mean, peak and time. To select the wanted mode, press
the shift key or select mode from the pop-up menu.

Ping mode
Displays the intensity as a function of range in the ping pointed at with the mouse in the
echogram. Only the visible range in the echogram will be displayed. If the echogram range
is zoomed, the oscilloscope range will be zoomed as well. If a layer is defined in the
echogram, only the range between the layer lines will be displayed.

Mean ping mode

Displays the mean intensity of all pings within the selected rectangle in the echogram.
Draw a square in the echogram around the region to be studied. Mean values of this region
will be displayed. The mean values will be calculated in the linear or the logarithmic
domain. This depends on the selection in the system configuration dialog located in the
Utility menu. See example 1 below.

Peak mode
In this mode the highest echo value found in each ping will be displayed. Draw a rectangle
in the echogram around the echoes to study. Peak values will be detected within the
selected region. This mode can be used to extract data from experiments like fish in
carousel etc. See example 2 below.

Time mode
In time mode the oscilloscope window displays the intensity as a function of time at a
selected range. Click with the mouse in the echogram to select a range.

Size distribution mode

Sort all samples in a selected region according to size and present it in a histogram with
size as x-axis and count as y-axis.

Figure 200. Oscilloscope plot when size distribution display mode is selected

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Examples
Example 4: Extract the mean peak-value from a target in mean mode
Open an oscilloscope window in mean mode. Select the region to be analyzed in the
echogram window by drawing a square with the mouse. The Oscilloscope will then show
the mean intensity values from successive range bins as a function of range. The highest
value and its range will be displayed in the top panel. This result will be copied to the clip
board if the C-key is pressed. See Figure 194.

Example 5: Extract the intensity along a target in peak mode.

This function can be applied e.g. to study TS versus fish aspect and TS stability in
stationary targets experiments. To extract the change in intensity with time, open an
oscilloscope window in peak mode. Activate the echogram window and select the region to
be analyzed. The peaks within this region will be displayed in the oscilloscope. Activate
the oscilloscope and press the c-key. Start or switch to the program that shall receive the
data and paste the data to this program. Selecting the region in the echogram window can
be done in two ways. a) Draw a square around the region to study. b) Define a layer around
the echoes from the target. Activate the Tracker windows SED-page and select the all file
and manual tracking before pressing the start button. All pings in the file within the defined
layer will then be analyzed. See Figure 201.

Ping Peak(dB) Range(m)

490 -55.7 7.38
491 -52.3 7.44
492 -55.8 7.41
493 -56.1 7.38
494 -57.0 7.38
495 -55.7 7.47
496 -56.1 7.38
497 -56.8 7.38
Table 13 Part of a table exported from the oscilloscope window.

Figure 201 Peak mode. Development of TS from a single target lowered trough the beam
from a horizontal mounted transducer in a shallow pond. The picture has been exported
from the oscilloscope window by the top panel copy button.

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Play the echo on the sound card

Sonar5’s Oscilloscope window can now play each ping on the sound card. The function
simply sends the samples from the ping pointed at by the mouse in the echogram window
to the sound card. Zooming and layers control the layer presented on the sound card. Open
an Oscilloscope window from the analysis => Data insight menu. Press the right mouse
button in the Oscilloscope window and click the “Play ping on soundcard” in the appearing
popup menu. Then point at a ping in the echogram with the mouse. Note that the
oscilloscope must be in range-mode, which is default when opening a new oscilloscope
window. The samples presented in the oscilloscope and on the sound card are the same.

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Main menu

ABOUT ...................................................................................................................................................................382
OPERATING THE 3D-ECHOGRAM............................................................................................................................382
Top panel controls ...........................................................................................................................................382
2D presentation ................................................................................................................................................384
POPUP MENU ..........................................................................................................................................................384
DISPLAYING DIFFERENT ECHO EVENTS AT THE SAME TIME ....................................................................................385
ANGULAR ECHOGRAMS AND SYSTEM TESTING ......................................................................................................385
CROSSFILTER TEST ................................................................................................................................................386
Operating the Crossfilter tester........................................................................................................................387
But will adaptive threshold be fair? .................................................................................................................389
TUNING THE CHART PRESENTATION, AXIS TITLES, DECIMALS ETC. ........................................................................389
WHY DO I NOT SEE ANY THING PLOTTED? ..............................................................................................................390
OPERATORS AND METHODS ...................................................................................................................................390
Running windows .............................................................................................................................................370
Defining the plotting function f(x) ....................................................................................................................370
Operators .........................................................................................................................................................370
Mean ................................................................................................................................................................371
Var ...................................................................................................................................................................371
Sqewness ..........................................................................................................................................................371
Kurtosis ............................................................................................................................................................372
Correlation .......................................................................................................................................................372
Gradients..........................................................................................................................................................372
Autocorrelation ................................................................................................................................................372

Figure 202. Two objects, probably salmons moving upstream river Tana summer
09.07.1999. Resolution 9 cm / sample, smoothed with the built in running mean window
adjusted to 3x7 (samples x pings).

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About
The 3D echogram can display the echo intensity and in the case of split beam data, also the
sample angles in 3D charts and also in 2D graphs. The charts can be smoothed. Various
statistics such as variance, sqewness and kurtosis can also be presented. The input and
output can be logarithmic or linear and the results can be exported in various ways.

Operating the 3D-echogram

Selecting a region with the mouse in the echogram or setting up a region in the analysis
control dialog and pressing the analyze button will generate an analysis message. When
this message reaches the 3D echogram it will tempt to present the data as described in the
3D echograms top panel. Since presenting echograms in 3D are computational intensive it
is recommended to start with a small region. Scale and rotate the resulting 3D echogram to
show the wanted aspect before selecting a larger region. The top panel has controls for
controlling what and how data shall be presented. The source selector enables selection of
angle as well as intensity. To present angles, the phase file, with the extension .phase, must
be available in the same folder as the echogram. To plot the selection in the ordinary
echogram as it is, set: operator = Mean, window size = 1x1, factor=1, log(input=on),
log(output)=off

Top panel controls

Figure 203. Control panel 1. This panel controls the chart, the size of the running window
operations, what to present and how.
The top panel and the popup menu (right mouse click) control the 3D echogram. The top
panels have a mixture of selectors and control buttons for defining the wanted formula and
how to present it. The controls in this panel can set up the following formula.

f ( x)  Factor  logOperator log( x)

Where x=input Sv or TSu samples and f(x) = output data to be plotted. The factor and
threshold values, the log functions and the operator are set by the user. If f(x) is below the
threshold value the result will be replaced by the threshold

Source selector
Source can be Amp, Alo or Ath where Amp = amplitude intensity in form of Sv or TS
depending on what the ordinary echogram displays. Alo and Ath means along ship or
Athwart ship sample angles in degrees. These two sources will be available for split and
multi beam if the .phase files are available Phase files are generated during conversions if
the phase file checkbox is checked on. See section 3c additional information in chapter 5-
Converter for information about phase files needed to present angle samples.

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Operator selector
The operator selector selects window operators such as mean, variance, sqewness and
kurtosis. Note that for other values than the Mean, the window size must be larger than
1x1. This is because one cannot calculate e.g. variance from 1 sample. See the section
Operators and methods further down in this chapter for a detailed description of the
different operators.

Chart commander and display controls

The top panel has buttons to rotate, scale, print, copy to clip board and to edit the chart.
Pressing the edit button opens chart editor with a waste number of display options. Here
nearly every thinkable setting can be changed. See the section: Charts, in chapter 2 for a
general description of the chart.

Invert range check box

Checked on the range will be reverted. This can be convenient if one want to study the
increasing intensity from a bottom echo
Disconnect check box
This checkbox disconnect the 3D-Echogram from SonarX's message system. Use this
option to freeze a picture when you want to compare different echo phenomena from
different parts of an echogram or from different echograms.

Grid lines check box

Uncheck this to remove the support grid lines in the chart. If a large number of samples are
presented the 3D echogram may look nasty and black because of the number of gridlines.
Turning the gridlines off will clear the echogram and also increase the updating speed.

Figure 204. Turning of the gridlines and rotat the view into a 2D chart provides an
interesting presentation option.

Mark region in echogram check box

This checkbox is connected to the checkbox in the echogram control dialogs marker page
and turn this on or off. When checked on, the echogram will present a frame around echoes
that are applied to produce the presentation in the 3D echogram.
Window (h, w) selector
This two edit boxes controls the size of the running window operator. The first selects the
window height in number of samples or range bins and the second the window width in
number of pings. A window with size 3, 5 is three samples high, 5 pings wide, and covers a
total of 15 samples.

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The window The samples and the pings edit boxes define the size for the running window
operation that forms the 3D-echogram. Samples indicate the number of samples in the
range domain while pings define the number of pings to be included to produce an output
pixel. Setting both to 1 will present an unfiltered Amp-echogram or angular echogram. To
present mean or higher order statistics, at least one of the edit boxes must contain a value
greater than1.
Threshold edit box
If the pixel values in the information to be displayed do not exceeds the threshold value,
the threshold value will be presented for that pixel.

Factor edit box

The factor will be multiplied to the output result. For some situations the output is too
small for the chart to be able to present the result values along the left axis. Increase the
factor to see the results.
Log in and out check boxes
When checked the selected 3D-echogram will be presented in a logarithmic way. The log
(input) controls whether the input to the selected operator will be the plain Sv or TSu
samples or the linear domain 10Sv/10 or 10TSu/10 samples. The log (out) controls whether the
output will be logarithmic or not. The chart title will indicate the selection.

2D presentation
Although the name of the window indicate that it presents data in 3D it can sometimes be
convenient to switch the presentation to 2D The chart commanders 3D button control
whether the data will be presented as a graph in 2D or in 3D.

Popup menu

Figure 205. Point at the 3D-echogram window and press the right mouse button to open
the popup menu.
Help opens this chapter. Title let the user add a title to the 3D-echogram. Color toggles
between using color from the echogram color bar or from internally defined colors within
the chart. Show commander displays the top commander panel.

Help
Opens this chapter. For more help about the chart, see the section chart in chapter 2.

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Export
The chart and the data can be exported in various ways with this menu. Note that an
alternative export function is found in the charts editor. To use this, see see the section:
Charts, in chapter 2.
Export Entire window
Copies the entire 3D-echogram to clip board as a bitmap. This will include the control
panels indicating how the figure was created, the size of the running mean window etc.
Export Chart only
Copies the chart as a bitmap.

Export Peak data values

Copies detected peak values from the displayed echogram. Ping numbers, range and echo
intensity is extracted. To copy the chart, press the copy button in the control panel.

PingNr Range(dm) Amplitude dB

532 13.0 -29.9
533 13.0 -36.7
534 13.0 -35.5
Example 6. Table copied by the copy to clip board menu
Export Data with and without labels
This option will export the data plotted in the chart.
Clone window
This menu makes a copy of the 3D echogram window. It is currently not a true clone that
will appear and some settings may have to be set manually.
Add title
If a special title is wanted before exporting, use this menu. The title will disappear next
time the chart is updated with new information.
Use echogram color definition
When this menu is checked on, the colors in the echogram color bar will be applied.

Displaying different echo events at the same time

If two 3D-echograms are opened from the analysis menu, both will display the same echo
information. To display different events, present the first echo event and then disconnect
one of the charts by selecting the disconnect menu. Selecting the region containing the next
event will now only update the other 3D-echogram. To disconnect, select disconnect in the
popup menu.

Angular echograms and system testing

Studying the angular domain can reveal the quality of a recording. It can also serve as a
test for the transducer, the cables and the phase detector in the echo sounder. Testing is
especially important in a shallow river where one transducer position may result in very
poor phase results while a small change in the tilt may improve the result dramatically.

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Figure 206. 3D-Athwart ship angle domain. The trace from a fish is clearly seen.
It can be difficult to see if one of the four wires from the transducer is broken or if signal is
leaked from a wire to another (crossover). Studying a file recorded early in the survey with
the 3D-echogram in the different modes can reveal the errors and save the entire project.
E.g. the older transducer cables from Simrad can absorb moisture during a long term
monitoring project with crossover as the result. This is not seen on the echo sounder
screen.

Crossfilter test

Figure 207. The Crossfilter test display mode.

To switch between the 3D echogram mode and the Crossfilter test mode, right click and
use the popup menu to check the Crossfilter test menu on or off.

The Crossfilter test display mode is designed to study the effect of the Crossfilter
parameters in both 2 and 3 dimensions. The figure above displays how a particular setting
will detect targets in ping 266. The dashed line is the noise controlled adaptive threshold
whole the solid line is the smoothed output from the foreground filter. We can clearly see

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that the threshold follows the noise level and cuts through the two fish echoes in the middle
and to the right in the chart.

Operating the Crossfilter tester

Trim and transfer buttons

The Crossfilter detector has a button named trim setting. The 3D-echograms Crossfilter
tester has a Test and a Transfer button. If the Trim setting button is pressed in the
Crossfilter detector, a 3D-echogram will be opened in Crossfilter test mode with the same
parameters as set in the Crossfilter detector. This window is designed to help the operator
trimming the Crossfilter detector. After trimming, pressing the 3D-echograms Transfer
button will transfer the tested parameters back to the Crossfilter detector.

How to trim
Selecting a region in the Amp-echogram with the mouse will show how the Crossfilter
detector works on the selected region. By default, only one ping is presented. This ping is
marked in the Amp-echogram and indicates with ping number in the 3D echogram’s
Crossfilter test. Changing any settings in the 3D-echograms Crossfilter tester will
immediately update the test. The operator should test a selected set of targets which may be
difficult to detect due to size and noise, and tempt to find a setting where the dashed line is
cut through by the wanted targets. Alter the setting of the foreground and background
filter and the offset may result in a setting that can manage to detect most or all of the
problematic targets. If not, include the variance by checking the variance checkbox and
continue the search for an optimal detection setting.

Test button

Pressing the test button will transfer the current setting to the Crossfilter detector and run
this detector in test mode.
Include evaluation checkbox
The include evaluation checkbox influence on how the test button will work. If checked all
options selected in the Crossfilter dialogs step 2 will be applied in the test. If not only the
Crossfilter at the Crossfilter dialogs step 1 will be tested.
Arrow keys

The left and right arrow keys enable moving the test zone one and one ping to the left or to
the right in the echogram.

Variance checkbox
This checkbox opens the variance panel. Variance can be applied to extract more detection
power from the echogram. The variance is subtracted from the threshold line and can
generate a dip in the threshold line at positions where the fish are located. This can “drag”
a fish out of the noise. Use the “View added values checkbox to see what the variance can
do to the threshold.

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To test the settings on different pings

Figure 208 If the Variance is checked the variance panel will be visible and included in the
generation of the threshold line. Use negative values in the factor.
3D-view checkbox
Clicking this will show what the Crossfilter detector will detect in the selected region of
the Amp-echogram .
View added values checkbox
This will present the output from the variance panel only. In order to increase detection
power, variance must be high for wanted targets and low elsewhere.
Constant threshold checkbox
If checked, a threshold edit box will appear to the right for the checkbox. The adaptive
threshold line seen as a dashed line in Figure 207 will be replaced with the constant line
having the threshold indicated by the threshold edit box. This can visualize whether the
adaptive threshold line from the Crossfilter will work better than a traditional constant
threshold or not.

Figure 209. Upper chart: Constant thresholding of two targets. Lower: adaptive threshold
of the same targets.

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But will adaptive threshold be fair?

A fish passing the beam will have variations in the ping to ping TS due the swimming
pattern. A small fish close to a constant threshold will perhaps have some echoes below
and some echoed above the threshold. Echoes below will not be detected. This cause ping
gaps. A track with many missing detections are difficult to track. It may be split up in
many small tracks or it may be overlooked entirely. Adaptive threshold has a much better
chance to obtain more echoes from the targets than a constant threshold. More information
is always better than less, and we can always apply a constant threshold to the detected
targets later.

Figure 210. A King salmon (solid line) and an adaptive threshold line (dashed line). x-
axis is range in meters while y-axis represent arbitrary echo intensity.
In the this example, the echogram intensity (solid line) has been smoothed with a 33x1
filter and subtracted the variance multiplied by 6 and added a constant of 10. The variance
was found from sigma in square cm with a running window of 5x3. It is the variance that
produces the dip in the dashed line at the range of the salmon.

Tuning the chart presentation, axis titles, decimals etc.

Titles
It can sometimes be tricky for the chart to place the axis titles correct. To change the
placement of the titles,
1. Press the chart edit speed button to open the chart editor.
2. Select chart tab
3. Select Axis tab and the axis in question.
4. Select Label, Style and change the size. Increased label size will push the axis title
away.
5. Select Text and add space before or after the title. This will, however, be reset for
the next presentation.
Decimals and number formats
The edit button in the chart commander opens the chart editor. Here, a waste number of
options are available from color settings to labels and label formats.
For example, if one plot sigma the default setting with three decimals may not be
appropriate. Click the chart edit button and select Axis=>Left Axis=>Labels=> Format to
select more decimals or exponential formats. An alternative is to use the top panel factor

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edit box. A factor of 4*Pi*10000 will present sigma in cm2.

Why do I not see any thing plotted?

If threshold is set above the highest result value or if log(output) is on in a situation where
the operator produce negative values, then the chart will not plot anything but a constant
plain surface.

Operators and methods

Running windows
A running window is a matrix which is moved to all possible position on a larger matrix.
The Amp echogram is regarded as a huge matrix with samples in rows or rang bins and
samples in columns or pings. An echogram consisting of 1000 ping and with individual
rang bins covering 0.1m will, if the max range is 10m consist of 10/0.1 rows and 1000
columns. The echogram matrix size will be height x width = 100 x 1000. If we now for a
small running window with size= 3 x 3 and place that in the upper left corner of the
echogram matrix, it will cover 3 x 3 = 9 samples taken from 3 rang bins and 3 pings. We
can now calculate whatever we like from this 9 samples and plot the result as the output
3D echogram matrix position [2, 2]. We then move the running window so that its center
will cover position [2,3], collect our 9 samples again and produce a new output.

Range bins
1
2
3
1 2 1 4
3 4 3 5
2 1 1 6
7
8

1 2 3 4 5 6 7 8 9 10 11 …….Ping

Figure 211 Echogram matrix with a 3x3 running window with centered at position [5,4].
From the 9 samples selected by the runing window, we can find the mean, variance, kurtosi
etc. and plot the result in a 3D-chart at position 5,4. For this excample the mean value at
position [5,4]) will be mean[5,4]=(1+2+1+3+4+3+2+1+1) / 9 The values are example
values. For a real echogram they would be values like -40 dB or 10-40/10 if log(input) is
turned off.

Defining the plotting function f(x)

The 3D echogram can plot the echogram data in various ways. In the following we will
denote the samples fond in the amplitude echogram as Input or Input[j,i] when we discuss
a specific sample in range bin j and ping i. Input will contain either Sv or TSu values
depending on what the echogram has been set to display. Use the Echogram =>TVG menu

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to change between Sv or TSu. Subscript u for uncompensated denotes that the values are
not off-axis compensated.

 Factor  logOperator log( x) f(x)  threshold

f ( x)  
threshold f(x)  threshold

Where x=input data and f(x) = output data to be plotted. The factor and threshold values,
the log functions and the operator can be set by the user. This enables presentation of the
following outputs among other functions.

If we assume that the amp echogram contain TSu values, then

Operator Window Factor log(input) log(output) Output
Mean 1x1 1 on off TSu (dB)
Mean 1x1 1 off off ts = sigma_bs
Mean 1x1 6.28 off off 6.28*ts = sigma_sp
m2
Mean 1x1 62800 off off 62800*ts = sigma_sp
cm2
Mean 3x3 10 off on 10 log(mean(ts))
Mean 3x3 1 on off mean(TSu)
Var 3x3 10 on off 10log(var(ts))
Kurt 3x3 10 on off 10log(Kurt(ts))
Table 14 Some presentation possibilities. ts = 10TSu/10

Operators
In the following operators are found in the Operator selector. Let H and W be the height
and width applied by the operator and define
h  ( H  1) / 2,
w  (W  1) / 2
N  H W
And X denotes the input samples Then we have

Mean
1 r h l w
meanr , p    X i, j  X r , p
N i r h j c  w1

Var
1 r h
X 
l w
Varr , p   
2
r, p  X i, j
N  1 i r h j c  w1

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Sqewness
X 
r h l w
Sqewr , p 
1
 
3
 X i, j
Varr , p  1 i r h
1.5 r, p
j c  w1

Kurtosis
X 
r h l w
Kurt r , p 
1
 
4
 X i, j
Varr , p  1 i r h
2 r, p
j c  w1

Correlation

r h l w
  (X i 1, j  X )( X i , j  X )
Corr r , p  
j r h i c  w1
r h l w
  ( X i, j  X ) 2
j r h i c  w1

In Excel format, cell D at an arbitrary row with w=3 and h=1, the nominator will be:
=((C5 - average(C5:E5)) * (D5 - average(C5:E5) ) + (D5- average(C5:E24)) * (E5-
average(C5:E5)) )

Gradients

r h l w
Gradient _ hor r , p  
1
N
  ( X i 1, j  X i , j )
j r h i c  w1

r h l w
Gradient _ vertr , p  
1
N
  ( X i , j 1  X i , j )
j  r  h 1 i c  w

Autocorrelation
The autocorrelation function plot the correlation between the signal and the signal
displaced with increasing displacements. This can give important information for example
about the noise in an echogram. If the noise is totally uncorrelated (white noise) the
autocorrelation function will drop to zero immediately. To find the autocorrelation in the
ping domain, the mean is first found for the selected number of pings P at each range bin r.

1 B
Xr   X r ,i
B  A i A

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Where A is the first and B is the last selected ping to evaluate. Autocorr is found for
increasing delay number for each range bin r and plotted

B  MD
 ( X r ,i  X )( X r ,i  d  X )
AutoCorr r , p, d   i A
B
 ( X r ,i  X r ) 2
i A

Where MD is Max Delay. Repeating the calculations for all selected range bins and for all
delays from 0 to the selected Max Delay can result in a plot like the following:

If the 3D button is deactivated by clicking, then the chart will show the average correlation
in the selection.

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Main menu

ABOUT ...................................................................................................................................................................395
ANALYZING ECHOGRAMS ......................................................................................................................................396
COMPONENTS GROUP 1, MAIN CONTROL ................................................................................................................396
COMPONENTS GROUP 2, THE DIMENSION SELECTION RADIO PANEL .......................................................................397
COMPONENT GROUP 3, THE SED FILTER RADIO PANEL ..........................................................................................397

Figure 212. The sample data analyzer dialog.

About
The dialog was originally developed for insight into EY500's dg files but has now been
upgraded to work with Sonar5 files from all echo sounders. The .phase file must have
been extracted during conversion.

The sample data analyzer was designed to study why the single echo detector in the EY500
produced fish tracks with larger ping gaps and more surrounding noise echoes when the
transducer was aligned horizontally in shallow rivers than in vertical open water situations.

The module is useful for studies of sound behavior and for equipment checking.

To calculate correct values from the sample data it is important that the sonar parameters in
the parameter dialog are correctly set. The module is accessible for those want to use it, but
the dialog will not be developed further and we will not write a detailed manual to explain
its functions.

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Analyzing echograms
Drawing a rectangle with the mouse around some echoes in an echogram will send an
analyze message to the sample data analyzer. If available the sample data analyzer will
open the original DG file and read the power and angle samples from the selected region.
The user can select whether to display the sample power or the sample angle data
graphically in two or three dimensions. A peak detector will detect peaks and send
messages back to the echogram where the locations of the peaks will be indicated.

String grids will show the actual sample power and sample angles from each pulse together
with single echo detector criteria calculated from the sample data.

Components group 1, main control

Figure 213. Control components

Scrollbar located in the top left corner

If the Show 3D checkbox is checked of, sliding the scroll bar will control what ping to be
presented in the chart. The echogram will mark what the chart presents.

dB snr.
All samples with intensities in the interval between the peak and the peak-snr will be
analyzed. Snr=6 dB will present the pulse as obtained by the single echo detector.
Snr=base threshold will present all.

dB Threshold.
Base threshold for the analysis. No echoes below this threshold will be presented.

Disable In check box

Disable input from the echogram.

Show statistics not samples

When checked the single echo detection parameters and statistics are displayed, otherwise
the actual sample values are presented for the ping selected by the top left scroll bar.

Show 3D checkbox
When checked the selected region is presented in 3D. If not, the samples in the ping
selected by the top left scrollbar is presented in 2D.

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SE instead of Std
When checked the standard errors are presented and not the standard deviation in the along
ship and athwart ship sample values.

Nr. samples.
Determines the number of samples to be analyzed. If set to zero, the region selected with
the mouse in the echogram will be valid.

Nr. Ping.
Determines the number of pings to be analyzed. If set to zero, the region selected with the
mouse in the echogram will be applied.

Components group 2, the dimension selection radio

panel

Figure 214. Dimension election

Alo radio-button
If selected the along ship angles will be presented

Ath radio-button
If selected the athwart ship angles will be presented

Amplitude radio-button
If selected the amplitude samples will be presented

Angle magnitude radio-button

If selected the magnitude between the along ship and athwart ship angles will be presented

Differentiate check-box
If checked the differential signal will be presented.

Component group 3, the SED filter radio panel

Figure 215. SED-filter

Show all samples radio-button

If selected, samples from all pings are presented.

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Show only missing SED radio-button

If selected only samples from pings where the SED detector has failed, will be presented.

Show only detected radio-button

If selected, only samples from pings where the SED detector did not fail will be presented.

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Main menu

ABOUT ............................................................................................................................................................. 399

BACKGROUND ................................................................................................................................................. 400
THE CROSSFILTER DETECTORS CONTROL PANEL ............................................................................................. 400
DETECTOR PART .............................................................................................................................................. 402
EVALUATOR PART ........................................................................................................................................... 403
Evaluators step 2a Fix cracks .................................................................................................................... 404
Step2b parameters, removing unwanted targets ........................................................................................ 405
Evaluators step 2c Fix cracks .................................................................................................................... 406
TUNING PARAMETERS ...................................................................................................................................... 406
Preparation, defining training set. ............................................................................................................. 406
Tuning the Detectors parameters ............................................................................................................... 407
Tuning the Evaluators parameter .............................................................................................................. 407
CROSSFILTER SINGLE ECHO DETECTION .......................................................................................................... 408
How single echoes are obtained from detected regions ............................................................................. 395
CROSSFILTER TRACKING .................................................................................................................................. 396
Advantages with Crossfilter tracking ......................................................................................................... 396
CROSSFILTER TARGET – NOISE SEPARATION ................................................................................................... 397
SED-Noise reduction.................................................................................................................................. 397
AMP-Noise reduction ................................................................................................................................. 413
Target removal ........................................................................................................................................... 413
Not transferred echoes shall be .................................................................................................................. 413
Apply to all frequencies check box ............................................................................................................. 414
Masking button........................................................................................................................................... 382
Apply to all frequencies checkbox .............................................................................................................. 382
CROSSFILTER NOISE LEVEL DETECTION ........................................................................................................... 382

About
The ability to detect a target is a key point in handling acoustic data. A detection can be
applied for various tasks such as
 Generating single echoes and form a new SED echogram
 Track and classify targets.
 Remove unwanted targets such as fish if one wants to study plankton.
 Remove all targets and obtain the noise level.
Hence, it is important to be able to detect something.

The detector consists of three parts.

 Step 1. Detector. Does the detection.
 Step 2. Evaluator. Refines and evaluate the detections. Unwanted detections are
removed
 Step 3. Task. Uses the detection for something such as SED, tracking etc.

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Terminology and image analysis commands presented in this chapter are explained in
chapter 15-Image analysis.

Background
Traditional single echo detectors based on echo length followed by an evaluator tend to fail
in situations where the signal to noise ratio is low, e.g. in horizontal shallow river
applications and small target studies in open water applications. Too few echoes are
detected from passing fish. At the same time to many echoes occur in positions where no
single targets can be observed. Adjusting the SED criteria to accept more echoes from fish
increases the number of erroneous detections. Adjusting the SED criteria to discard more
noise increases the number if of missing detections from fish. By "traditional" we mean a
detector analyzing echoes from one and one ping by a set of criteria such as echo length,
shape, intensity, and phase deviation.

Studying sample power and sample angle telegrams from EY500 has reviled that echoes
from fish in noisy environments such as a river frequently have echo length longer or
shorter than the expected echo length. Multiple peaks, high phase deviation and ping-to-
ping variations in the intensity are also common. With the traditional SED criteria, fish
echoes looks like multiple echoes, while background noise frequently looks like single
echoes. This study is reported in Balk and Lindem (2001 c)

The idea to the Crossfilter detector was presented at the SWFC conference in Seattle in
1999.

The first actual Crossfilter detector was presented in Montpellier Jun 2002 under the title:
A new method for single target detection. (Balk and Lindem 2002)

To understand the Crossfilter detector, listen to the speech from the Fast meeting at Bergen
June 2003. This speech is located in the folder
Balk_Lindem\Program\Help_Articles\Balk_Lindem_2003\Fast_2003 if installed or on the
SonarX CD in the same folder. (Powerpoint must be available).

The improved Crossfilter detector described in this chapter was presented at the Jasa / Casa
meeting in Vancouver 2005 and at the AFS meeting in Anchorage in September 2005. This
presentation is found in the folder
Balk_Lindem\Program\Help_Articles\Balk_Lindem_2005

The Crossfilter detectors control panel

Test button
Press the test button to see how the default parameter setting performs (a temporary

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echogram is created)
Run button
Press the run button start the process indicated at in the caption and by the step 3 page. The
process will vary from single echo detection to tracking depending on from where the
dialog was opened. If it was opened from the Analysis => PreAnalysis => SED menu the
dialog will indicate that SD will take place. If opened from the Analyze => Setup =>
Tracking => Crossfilter tracking, Tracking will take place, and so on.
Generate commands Checkbox
If checked no actual process will take place, but the commands for the process will be
written to the trackers image page. Here they can be edited further to create methods not
creatable with the templates.
Process all selected files
If checked the process will process not only the echogram file opened at the moment but
all the files that was selected in the file open dialogs.
Open result file checkbox
If checked the dialog will open the resulting file after the new file has been generated.
Copy to clip board button
Copies all parameters in a readable text format to clip board.
Default setting button
Resets the Crossfilter according to a suggested default setting found to work well in many
cases.
Load button
Loads a setting from file.
Save button
saves the current settings to file. If the Auto save check box is checked on, Setings are
saved each time the Run button is pressed.

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Detector part

Figure 216. Crossfilter Step1 Detector page

The Detector page visualizes the signal flow. As seen, data is taken from the Amp
echogram and sent through two filters and a variance panel. The output from the
background filter is added an offset to form a background threshold. If variance is checked
the variance is added to the resulting threshold as well.

Foreground filter.
 The filter reduces ping-to-ping fluctuations in the echo intensity from the fish track.
With other words, energy from strong parts of the track is moved to weaker parts. This
reduces the chances that some parts will fall below the applied threshold, resulting in
missing detections.
 Spikes or peaks in the background intensity will be reduced. The effect is that the
chances that these unwanted peaks are detected as single echoes are reduced. Ping gap
in tracks from fish combined with surrounding noise detections makes tracking
difficult or impossible.
Background model
The next step is to obtain a background model. This can be done in two different ways,
either by applying a fitted mean filter or by detecting the loacal median for each range bin.
A selector in the top of the background boxs enables selection of the two methods.

Mean filter method

Studying echo samples from one ping as a function of range shows fish echoes as thin
spikes on top of a slowly varying background. Applying a low-pass filter with a low cut of
frequency in the range domain will remove most of the fish echo and preserve the slow
variations.

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App. Median method

App median means approximated median. The method was proposed by McFarlane and
Schofield in 1995. This method is implemented because it is much faster than ordinary
median. The median is built up by comparing the background from the previous ping with
the intensity in the current ping. If the intensity at one sample in a rangebin is higher than
the intensity in the background, then a fixed number of dB are added to that rangebin in the
background model, and vice versa if the foreground intensity is lower. The algoritm is
initiated by making an app. median from thje first 500 pings. How much the algoritm shall
add or subtract from a sample at a rangbin in the background model is controlled by the
value in the strength edit box.This box appear only wnhen the App Median is selected.
High strength makes the bacround addapt to the forground faster. A fish staying in the
beam for a long time may become invisible in the end of the trace if the strength is set too
high.
Recommendation: when this method is selected we recommend that the foregtround filters
height and width both are set to 1 and that one apply a mean or median filter of some value
in the pre.op box. In this way the Cross filter detector will carry out background
subtraction as applied in many video systems.
Offset
The offset is added as a constant dB value to all samples in the background model.
Variance
If checked, variance will be obtained by a running window and multiplied by a factor. The
result will be subtracted from the threshold.
Combine
The signal from the foreground filter will only pass through this gate if it is stronger then
the Threshold. This signal is passed on to Crossfilters evaluator at step 2.

Evaluator part
The evaluator is an important part of the detector and that the Crossfilter detectors step 1
should produce detections in a way that can be separated by the evaluator. The signal flow
is presented graphically in the evaluator seen in Figure 217. Here we can see that the signal
comes from the Crossfilter detector step 1, and is passed through the evaluator step2a,
step2b and step2c if these are checked on. We do also see the step2b takes both detections
from the Crossfilter and data from phase file as input and output wanted detections.
Unwanted detections are deleted.

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Figure 217. Step 2 Evaluator page

Evaluators step 2a Fix cracks

Figure 218. Step 2a Fix cracks page

The echo intensity from a small target might fluctuate close to the noise level. The
fluctuations can cause cracks in the detected regions. These cracks can cause problems for
target remover in step 2b and for the method in step 3. Applying a smoothing filter can fill
cracks with echo energy from the surrounding regions and "glue" a cracked track together.
Increasing parameter values for a domain will increase the number of samples that will
receive energy from the detected region in that domain. By default the filter is set to
increase the regions in the horizontal domain only.

Image analysis command: Mean 1 3

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Step2b parameters, removing unwanted targets

Figure 219. Removing unwanted targets with the evaluators step 2B parameters
The remover can remove detected regions. Each line that is checked will add a size filter to
the process. The filter will remove detected objects if the object is smaller than the filters
min value and greater then the filters max value. Some of the filters can be compared with
traditional single echo detection criteria such as echo length, std. dev and TS. There are
however important to note that these filters work on the entire target and not on individual
pings. Hence, removing a target below Max or mean TS will not make ping gap in the
target if parts of the target is outside the limiters. Either the entire target is accepted or the
entire target is removed from the echogram. The filters are described in the size filter
section in chapter 15.
Ok button
Accepts the setting, closes parameter dialog and opens open the evaluator page.
Edit event button
Opens the Event editor. Use the editor to draw a rectangle around each target to be
accepted by the evaluator. Ensure that the rectangle includes all part of the target.
Auto detect button
Pressing the auto detect button will tune the evaluators parameters to the detections
obtained within each target framed by a rectangle event. Only checked parameters are
tuned.
Hint button
This button will open a quick help dialog telling how to use the evaluator.

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Evaluators step 2c Fix cracks

Figure 220. Crack fixing by growing.

A crack fixer be inserted after the target remover in step 2b. Persistent cracks can remain in
the echogram. In this page, two different methods are available, crack fixing by smoothing
and crack fixing by growing. The smoothing is identical to the smoothing for step2a above.
If the fix cracks by selector are set to smoothing a smoothing panel will be visible. In
Figure 220, growing has been selected. Growing means that a detected region grows into
the surroundings. The two first growing parameters can be applied to restrict the growing
to medium sized regions. Numbers of samples define how much the region will grow in the
direction defined in the direction parameter. The last parameter can have two values, Melt
or No melt. If set to Melt, two nearby regions are allowed to melt into one larger region.
This is normally what we want here.

Image analysis command: Grow 20 500 1 Width Melt

Tuning parameters
There is always a question about parameter setting. For the traditional single echo detector
based on echo length, one setting result in to many ping gaps and missing detections while
another results in to much noise. Perfect setting does simply not exist, and it depends on
our data quality, aim and application whether a setting can be said to give sufficient
detection and separation between wanted and unwanted targets. To obtain the best possible
setting it is important to understand the detector one is tuning. The echo length single echo
detector has two parts;- the detector and the evaluator. This is true for the Crossfilter
detector as well. Hence, we will first look at how we can tune the detector parameters and
then how we tune the evaluator parameters.

Preparation, defining training set.

When we apply the traditional single echo detector we normally test a few parameter
settings until we see that there is an acceptable balance between wanted and unwanted
detections. This works when we are dealing with “good” data, but it is highly subjective
when we are dealing with “difficult” data characterized with low signal to noise ratio. For
“difficult” data we strongly recommend that a training set is defined. This is done with the

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event editor. Set the echogram to show the amplitude echogram and set the threshold as
low as possible. Then study the echogram carefully and draw a rectangle event around the
targets to be detected. See the manual chapter 21 Events and vessel log. It is not important
to mark as many targets as possible, but it is important to mark at least one target of each
kind to be detected. The event editor’s event list will let you jump between the marked
targets simply by clicking the list with the mouse.

Tuning the Detectors parameters

The Crossfilter detector uses adaptive thresholding to detect echoes. A threshold is formed
to follow just above the fluctuating noise level. Echoes with higher intensity than the
threshold, are detected. The parameters involved in the detector part deals with improving
the signal and defining the threshold.
Echoes sticking up above the threshold consist of samples or small rectangles with
individual intensity. As with the traditional single echo detector, there will be two kinds of
detections, wanted and unwanted. A list of important guidelines can be stated.

1. All targets marked in the training set should be detected with as many connected
samples as possible. Connected means here that there are no separating gaps
splitting the samples into different regions.
2. Unwanted detections should be detected in with as few connected samples as
possible or with a shape that differ as much as possible from the wanted targets.
3. It is not important to avoid detecting unwanted targets, but it is important that the
unwanted targets look different than the wanted targets.
4. Remember that the evaluator following the detector only can filter out unwanted
targets if they differ from the wanted targets in a way that the evaluator can see.

To trim the parameters, use the Test button, the echograms zooming possibilities and the
event editor / browser. It is recommended to turn off the evaluator at step 2 to not be
confused about what is detected and what is removed by the evaluator. Check that all the
wanted targets marked in the training set is detected.

Use also the Trim settings button. This button will open the 3D echogram in the Crossflter
test display mode. This is mode is designed to visualize and assist in trimming the
Detectors parameters. See the section Crossfilter test in chapter 17 for more details.

Tuning the Evaluators parameter

Opening the evaluator, checking the step 2b box, and pressing the parameter button opens
the evaluator’s parameters. There are more parameters here than in a traditional SED
detector. One reason to this is that the Crossfilter detector detects the entire targets and not
only one and one echo from one and one ping. This gives the Crossfilter detector a major
advantage in the ability to separate wanted targets from noise and other unwanted targets.
There are two ways to trim the setting, manually or automatic. Selecting the parameters
one want to include and pressing the auto detect button will estimate the parameters
automatically from the training set defined by the event editor. Read more about the
evaluator in the section Step2b parameters, removing unwanted targets in this chapter. The
evaluator filters are described in the size filter section in chapter 15.

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Automatic trimming
1. Press the Edit events button and draw a rectangle around the targets you want the
filters to accept
2. Press the Auto detect
3. Press the test button to see if the new settings work as expected.

Notes
Parameters will only be detected for selected filters
Phase based filters will not be tuned and must be tuned manually
The tracker windows Image page has a check box named "All file"
Checked Off: visible events will be applied in the detection
Checked on : All events will be applied in the detection

Manual parameter trimming

1. Trim the filters one by one. Turn of all filters except one.
2. Start by setting max to some very high value
3. Set min to 1 and press the test button.
4. Repeat with increasing Min value until you start to remove wanted targets
5. Do the same with the max value.
6. Turn off the filter and turn on the next filter and repeat the process for the next
filter.
7. When all filters have been adjusted, turn on the filters that gave results.

Note that changing values on the Crossfilters 1 page influence on the way the size filters
works. If you can not find a good size filter setting, try to change the setting on the
Crossfilters first page and redo the process.

Crossfilter Single echo detection

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Figure 221. Step3 set up to perform single echo detection

Located in
Menu: Analysis => Pre-analysis => SED (Crossfilter detector).
Aim
The aim is to produce a SED echogram without missing detections from targets and
without noise detections.

About
The SED Crossfilter detector produces a new file containing the original Amp echogram,
but with a new SED echogram as indicated graphically in Figure 221. The method needs
the phase file to find the angular positions for the SED and to evaluate the quality for each
of the detections.

Echo separation panel

The Crossfilter detector detects regions in the echogram with high probability of
containing targets. The default setup reflects a situation where each region only is
supposed to contain one target each. We recommend this setting for most applications.

When the Fill gap checkbox is checked, interior holes in a detected region will be filled
with a value slightly above the threshold. This will prevent the detector algorithm to regard
a ping with two peaks separated with intensity below the threshold as a multiple echo. The
first peak will be the one that is detected.

There may be situations where a detected region can contain two or more fish. This is
sometimes the case in fixed location horizontal river applications where Salmons are
migrating in small groups. The checkbox “Allow region to contain more than one track”
can then be checked. If checked, an edit box with the label [ 1 ] pulse length between each
detection, will appear. This enables the operator to select a minimum detection distance
between each target. The Crossfilter detector will generate single echoes from the first
peak and the next echo from the next peak if this peak is sufficiently separated. The
detection continues throughout each ping but only within the region detected by the
Crossfilter detector.

Range detection panel

Determine range of a target from its echo pulse is a difficult task. Should range be set to
the start of the pulse and if so, what is the start? Should range be set according to the peak
or should we set it to the center of gravity? We have found that this depends on the signal
to noise ratio (SNR). For low SNR, such as we frequently see in horizontal shallow water
river applications, pulse start plus a fraction of the pulse length seems to work best. For
high SNR situations such as vertical recordings of fish with low density, center of gravity
works best. Peak is another possibility, but normally peak gives higher fluctuations in the
obtained range from a passing target than the other methods.

SED quality definition

The definition is located on the echogram control dialogs quality page. The button will

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open this page and enable setting of the definition. The definition looks similar to the
traditional echo length detectors parameters. Each detections made by the Crossfilter
detector is tested against the quality definition and if the echo is accepted according to the
definition, the echo is marked as a high quality echo. If not it is marked as a low quality
echo. The mark can later be applied for example to let the tracked track data with few ping
gaps and at the same time restrict low quality echoes from being used in the estimation of
sensitive calculations such as target strength, velocity etc.

Obtain TS for the SED echogram panel

TS is taken from the peak intensity of an echo pulse in the echogram that is selected in this
panel. The default source is the Amp echogram with zero Q’s in the extension. Each Q in
the extension indicates a higher processing level. Zero Q’s indicated the original echogram
containing TS or Sv values estimated in the traditional way with the equations presented in
Chapter 5. If the original echogram is influenced by noise, peak values may be much
higher than they should. It may then be an idea to smooth the echogram with filters before
estimating the TS. Run a low pass filter first and the select to take TS from the echogram
with one Q in the extension will do.

How single echoes are obtained from detected regions

The Crossfilter detects regions of echoes in the Amp echogram. Each region is separated
from other regions by samples below the base threshold. The algorithm analyzes one and
one column in the processed Amp echogram. A detected region may consist of series of
samples for a number of successive pings. For each ping, the algorithm searches from the
first sample rising above the base threshold until the last sample before the region returns
to the base threshold. Each peak on this way through a region is tested with a traditional
echo length detector set up with parameters according to the quality definition. This may
find none, one, or a few single echoes and mark them as high quality echoes. If no high
quality detection is found, a peak detector is applied to detect low quality echoes.

D1
D6

F1
D2

D3

D4 D5
F2

Stones
F3

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Figure 222. Left: SED echogram from a traditional SED detector trimmed to obtain
optimal balance between low noise and high track quality. Right: SED echogram
generated by the Crossfilter detector. D1..D6 and F1..F3 are the debris and fish tracks.
The figure is taken from (Balk and Lindem 2002)

Crossfilter tracking

Figure 223. The Crossfilter trackers step 3 page.

Located in
When the tracker window is available and CFT is selected as method, a setup button will
appear. Pressing the button will open the Crossfilter tracker.
Aim
Improve automatic tracking in cases where the SED echogram have low track quality
combined with many noise based detections.
About
The main problem for automatic trackers operating on single echoes is the missing
detections and the surrounding noise detections. This leads to all sort of erroneous tracks.
Tedious manual tracking is often the only possible way. With manual tracking, the
operator places the cursor in the echogram and encircles the echoes to be combined into a
track. Regions with noise and erroneous detections are not tracked.

This is exactly what the Crossfilter tracker does in an automatic way. The Crossfilter
detector finds traces and encircles them. All echoes in the encircled traces are converted to
SED and combined into tracks which can be stored in a fish basket.
Tracker panel
Atlantic salmon do some times migrate in small dense groups of may be 2 to 7 individuals
which can be difficult to separate into individuals. The CFT can then be set up to detect the
whole groups. Checking on the “Search for more...” checkbox will use the trackers Auto
MTT algorithm to track individual targets within the group. When checked, the MTT

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parameter panels will appear in the Tracker window where they has to be tuned for the
wanted task.
Classify panel with store track checkbox
Check this box on to store the tracks. If the classify window is visible, the fish baskets in
this window will store the tracks. The window can be set up with many baskets and the
baskets can be set up to filter what kind of tracks to accept. All features found in the
feature library are available for filtering. If the Classify window is not visible, the Classify
windows first basket will appear in the tracker windows fish basket panel.

Advantages with Crossfilter tracking

 Low noise. Echoes outside a region looking like fish will not be tracked. This
eliminates substantial amount of noise.
 No cross over. Echoes from one detected region cannot be combined with echoes from
another region. This reduces the chance of combining nearby tracks.
 No problem with tracking parameters. The tracker can be set to combine all echoes
within the detected regions. In some cases auto tracking might be applied, but since the
track ends when the region end, the tracking parameters such as gate and ping gap can
be set to accept far more than with ordinary tracking.

Crossfilter Target – Noise separation

Figure 224. The Crossfilter target - noise separator template is located in the Analysis =
Pre analysis=>Noise menu. Its purpose is to reduce noise or unwanted echoes in the Amp
echogram and to reduce the noise in an existing SED echogram.
Located in
Menu: Analysis => Pre-analysis => Noise => Target – noise separation
Aim
The aim is to generate a new file with an Amp and SED echograms where wanted or

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unwanted targets has been detected or removed. Examples can be removed fish when
plankton is the aim or removed macrophyte when fish is the aim. Results can be applied to
echograms recorded with other frequencies as a mask.
About
Noise is what we do not want. If we want to analyze plankton, fish is the noise. If fish is
what we want to analyze, echoes from plankton are the problem. In other cases we want to
keep some targets and get ridge of other targets. In a river echoes from fish are wanted but
echoes from stones are regarded as noise.

The principle for this method is that if we can detect something we are free to do what we
want with the detection. We can remove it, do nothing with it or remove everything except
it. This can be done both for the Amp and the SED echogram. This is demonstrated in the
dialogs graphical layout as seen in Figure 224

SED-Noise reduction
SED-noise is simply unwanted single echo detections seen in the SED echogram. These
can be detection of peaks in the background reverberation or echoes from unwanted targets
such as air bubbles. With too much SED-noise, biomass estimation and tracking will give
erroneous results. Hence, noise reduction is important. To reduce SED noise, select
Transfer all for the Amp echogram and Transfer detected targets for the SED echogram in
Figure 224.

If sample data is available, the SED (Cross filer detector) should be applied instead
because this detector both improve the number of detections from wanted targets and
reduces the SED-noise. The noise reduction method removes noise outside detected
targets, but does not improve the detections of wanted targets.

AMP-Noise reduction
AMP-noise is samples with echo intensity that contributes in an unwanted way to the echo
integral. This noise can be caused e.g. by plankton surrounding fish tracks, by unwanted
targets such as air bubbles and by reflections from surface and bottom. To get ridge of this
select Transfer detected targets for both the Amp and the SED echogram in Figure 224.

Target removal
A detected target can be erased from the echogram so that it do not influence on ether
tracking or biomass estimation. Fish can be removed is plankton is the aim, stationary
targets can be removed if fish counting in a river is the aim. Special noise phenomena can
be detected and removed as well. Erased targets are not permanently erased and can be
recalled one by one or all at once from the echogram control dialog’s noise page. To
remove detected targets, set the Transfer selectors to all but detected targets in Figure 224.

Not transferred echoes shall be

This selector determines what to do with not transferred echoes. Shall they be left there and
allocated a very low value, below any possible threshold or shall they be erased. The
biological meaning is that if we for example want to remove fish and estimate plankton,
and threshold the regions containing fish, then we say that the fish scared away the
plankton so that no plankton where expected in the thresholded regions. If we erase, we

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say that the fish did not suppress the plankton. Hence erasing will result in a higher
plankton estimate than the thresholding. For thresholded regions samples are counted but
they do not contribute to the echo integral. Erased samples do not contribute and are not
counted.

Apply to all frequencies check box

This will superimpose a mask on all other frequencies or channels in a multichannel file
set. It enable detecting and making a nose, fish or other target mask in one frequency and
apply that to remove targets in frequencies where detection is less simple due to a different
signal to noise ration. Read more about this in the masking section of chapter 23.

Masking button
Pressing the masking button will open the masking dialog. The button is placed there for
convenience and open the same dialog as the Multifrequency=> Masking menu. See the
Multifrequency chapter for information about the masking dialog

Apply to all frequencies checkbox

If this box is checked, the detected targets in the current file will be used to mask the same
targets, but in the other echogram channels. If plankton is the target and fish is unwanted
then fish may be best detected in the lowest frequency and not so easy to detect in the
higher frequencies. Then detecting fish in the lowest frequency and using these detections
to remove the same regions also in the other higher frequency echograms may be a good
working procedure.

Crossfilter noise level detection

Figure 225. Max range detection dialog.

Located in
Menu: Analysis => Pre-analysis => Noise =>Noise level detection.
Aim
Obtain a maximum max range line for horizontal applications.

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About
The max range line is similar to the bottom line in vertical applications, and ensures that no
targets are detected at higher ranges than out to the max range line. In horizontal fixed and
mobile application the beam may hit the surface or bottom at different ranges because of
shallow areas and roll of the boat. Weather and water quality may also change and
influence on the noise along transects. Hence, analyzing the data out to a constant
maximum range independent of the noise level will easily loos smaller fish at periods of
high noise, and favor larger. This will cause bias in the results. To avoid this, the max
range detector set the range according to the noise level, ensuring that the noise level in the
analyzed data never exceeded a predetermined level.

The max range detector works as seen in Figure 225. The echo intensity from the amp
echogram is smoothed and applied a threshold. The range where that threshold cuts
through the smoothed reverberation level determines the max range. Fish and other
wanted targets should not influence on this max range detection process and must be
removed. This can be done in two ways, a) by using the Crossfilter technique to detect the
fish and then enable the “Erase detections” function and or b) removing smaller isolated
regions after having applied the threshold but before actually determine the range. Range is
determined for each ping as the first occurring sample seen from the transducer after the
described processing.

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Main menu

ABOUT ...................................................................................................................................................................417
ACCESSING THE DIALOG ........................................................................................................................................418
WHAT IS NEEDED TO USE THIS DETECTOR ..............................................................................................................419
IMPROVING SED BY TRIMMING THE CRITERIA .......................................................................................................419
HOW TO SET THE PARAMETERS ..............................................................................................................................419
Biomass estimation ..........................................................................................................................................419
Tracking ...........................................................................................................................................................419
High and low SED quality................................................................................................................................419
THE TOP PANEL ......................................................................................................................................................420
SED DETECTOR PARAMETERS................................................................................................................................420
Filter panel.......................................................................................................................................................420
Detector panel ..................................................................................................................................................421
Evaluator panel ................................................................................................................................................421
Beam clipping panel.........................................................................................................................................399
Quality panel ....................................................................................................................................................400
ABOUT RECTANGULAR BEAMS...............................................................................................................................400

See section Single echo detection in Chapter 4 Analysis for an overview of single echo
detection methods.

About
The Single echo detector (SED) described in this chapter is the traditional detector based
on echo length detection. This is the most common detector. In many situations especially
in situations with low signal to noise ratio the Crossfilter single echo detector may work
better. See chapter 17.

Single echo detection (SED) is important for tracking and biomass estimation. Most echo
sounders have a built-in SED capable of producing files containing SED echograms.
SonarX can extract these echograms. In addition various SED detectors have been
implemented. See section Single echo detection in Chapter 4 for an overview of methods.

The Single echo detector based on echo length detection consists of three elements. They
are

a) Detector
b) Evaluator.
c) Beam clipping
d) Quality estimator

The detector detects echoes according to the echo length criteria. Detected targets are
passed on to the evaluator. The evaluator determines whether the echo can be accepted or
not. Here criteria such as min size and phase deviation will sort out echoes. From the
evaluator, the echoes are sent to the beam clipper. The beam clipper cuts off detections. If
a rectangular beam is selected, detections outside the defined rectangle will be cut out. If a

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circular or elliptic beam cutter is selected, echoes with gain compensation higher than
stated by the Max gain comp. will be clipped off. If the along ship and athwart ship half
beam angles are equal, a circular beam will be the result. Otherwise an elliptical beam will
be seen. To test this, set up the system for manual or simple tracking and select a large set
of echoes with the mouse in the echogram. If a rectangular beam was applied the SED
detections will fill the position diagram window in a rectangular manner.

The echoes that have passed the beam clipper will be tested for quality. This is simply
done by applying another but more strict set of SED detector criteria. Echoes being
accepted by both the criteria set in the SED detector and the criteria set in the quality
definition dialog are marked as a high quality echoes. Echoes only accepted by the
parameters in the SED detector are marked as a low quality echoes. Both low and high
quality echoes are stored in the new SED-echogram. There are many reasons to mark
echoes with quality. As an example, for tracking, it is important with as many echoes as
possible while for size estimation only high quality echoes should be applied. The
Echogram control dialog and the system configuration dialog controls how the high and
low quality echoes are to be used.

Figure 226. Echo length Single echo detector dialog step 1

Figure 227. Echo length Single echo detector dialog step 2

Accessing the dialog

The dialog is accessed from the main analysis menu. Select
Analysis>Pre-analysis => SED (Echo length detector)

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What is needed to use this detector

 Phase file. The phase file is generated during conversion if the Extract phase file check
box is checked. This box is located on the converters first page.
 Echo telegrams from Simrads 500 echosounder series are not well suited if they have
few samples per meter.

Improving SED by trimming the criteria

The test job button provides a fast way to see the result of varying the SED-criteria.
Open an echogram and locate some fish tracks. Pressing the Test job button will quickly
show the result on the displayed part of the echogram.

How to set the parameters

Biomass estimation
If we want to determine a fish size distribution (Biomass estimation) it is important to
eliminate as many multiple echoes as possible. Then strict criteria are important. Adjust the
parameters to avoid multiple echoes and noise based echoes from regions without fish.
Check this by comparing the SED and Amp echogram. It is less important to detect all
single fish or all echoes from all fish.

Tracking
If we want to track fish, we need as much detection as possible from each fish. Strict
criteria will increase the number of missing detections and may remove tracks completely.
To avoid this, less strict criteria can be applied. This will also increase the number of
erroneous detections from the background reverberation. If it is not possible to achieve a
satisfactory balance between track quality (missing echoes) and SED-noise, other methods
such as the Crossfilter detector should be applied. See chapter 19 Crossfilter detector.

High and low SED quality

Obviously we want both strict and not strict setting at the same time since some analysis
like tracking needs as well detected tracks as possible while estimation of biomass, TS etc.
needs high accuracy. This can actually be done by using the Quality definition system. Set
the criteria in the Single echo detector window (Figure 227) to accept as much detections
as possible without including too much noise. Then press the Param. button in the Quality
panel and set the quality sufficiently strict to give accurate TS and biomass estimation
results. When the single echo detector detects echoes, these echoes will be marked with
high quality if they pass the high quality definition and with low quality otherwise.
Checking the “Do not apply low quality echoes in analysis” checkbox found in the system
configurations general page (Press F9 or use the utility menu to access it), then detections
marked with low quality will be excluded from sensitive estimations, but can still be
applied in the tracking.

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The top panel

Test button
This button generates a test job. Only the visible part of the echogram is processed. The
echogram displays the results at once as a picture, but nothing is stored. The aim is to test
various parameter settings in a fast. When the test button is pressed, the SED template
dialog writes a set of commands to the Tracer windows image page. If the "Generate
commands" check box is not checked, the execution of these commands starts. Press the
appearing stop button if you want to stop the execution before the process finish.

Run button
This button generates a job that will produce a new file. The new file is marked with a
letter Q in the extension.

Generate commands checkbox

If checked, commands will be written to the Tracer windows command editor but
execution will not take place. The caption of the Run and Test buttons will change to
indicate this.
The checkbox enables the commands to be further edited before execution.
Process all selected files checkbox
If checked all selected files will be processed when the run button is pressed.

Open result file checkbox

If checked the last file processed by the Run button will be opened. Alternatively, press the
short key Alt+Q or use one of the file open dialogs to open a result file. Result files have
the same name as the original file but a letter Q is added to the extension each time file is
processed.

Load
Load parameter setting from file.
Save
Save the detectors parameters to file.

SED detector parameters

Filter panel
Filter check box
If checked, the low pass filter parameters will appear. Filtering may reduce ping gap in
tracks from fish and reduce erroneous echo detections.
Filter width edit box
Visible if the enable smoothing checkbox has been checked. Determines the low pass
filters cut of frequency in the ping domain. Increasing the filter width will lower the cut of
frequency. Values such as 3,5 and 7 have often performed well. The result will depend on

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the ping rate. Higher ping rates may demand higher parameter values.
Filter height edit box
Visible if the enable smoothing checkbox has been checked. Determines the low pass
filters cut of frequency in the range domain. Increasing the filter height will lower the cut
of frequency. Values such as 1, 3 (and 5) have often performed well. Even number should
be avoided.

The result will depend on the range resolution of the Amp echogram. High resolution such
as 3-cm per sample may work better than low resolution

Detector panel
Min. Echo Length edit box
If the echo length is shorter than this value, the echo will not be detected. Echo length is
measured relative to the transmitted pulse.

Max. Echo Length edit box

IF the echo length is longer than this value, the echo will not be detected. Echo length is
measured relative to the transmitted pulse.

Evaluator panel
Threshold edit box
Minimum fish size measured dB. The fish size is corrected for off-axis loss and then
compared with this parameter. Echoes with intensities below the threshold will not be
detected.
Max. phase dev.
An echo may consist of more than one sample depending on the sample frequency. The
standard deviation within all samples within one echo is calculated for the along ship and
the athwart ship domains. The highest value is selected and compared with the Max. Phase
Dev. parameter.
Warning: SonarX define Max. phase dev. different from Simrad in that the parameter is
calculate from angle samples measured in true degrees and not in internal electrical phase
steps. To help users familiar with the Simrad way, most dialogs dealing with this parameter
has a converter that shows what the setting relates to in the 60 and the 500 echo sounder
series. Click on the line with the text “* Click this line to see how Max. phase dev. = 0.3 relates to
Simrads Max.phase dev. parameter.” opens the converter. The converter is descried in chapter 4,
end of section Analyse_Single_Echo_Detection
Separation
Separation sets the minimum accepted distance between echoes in the same ping. This
criterion can reduce the number of detections within dense fish schools a school where
single echo detections tend to detect fluctuations in the echo level and not the actual fish.
Trim the parameter to preserve clear fish tracks and reduce scatters from bottom and
schools.

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Multiple peak combo box

The operator can select three options here; off, medium and strong. Select off to turn off
the test. Medium accept multiple peaks with local min values less than -1.5dB. Strong will
not accept multiple peaks at all.

Beam clipping panel

This panel has a selector for the shape of the beam and parameters to set the beam size. If
the transducer is an elliptical transducer, the option will be elliptical or rectangular. If the
transducer is circular, the options will be circular or rectangular. If a circular or elliptical
beam is selected, the Max Gain comp parameter will be visible. If a rectangular beam is
selected, four parameters defining the rectangle will be seen.
Max Gain Comp edit box
This parameter restrict the off axis angles. Set to 3 dB indicates that no echoes will be
detected outside the -3dB beam.
Min and max beam angle edit boxes
When a rectangular beam is selected, the appearing parameters will contain edit boxes for
the min and max opening angles. Pressing the def. button will define the rectangle to the
angles noted by the -3dB opening angle parameters (half beam angles) located in the
calibration page.

Figure 228. The panel with the parameters for the recangular beam is only visible when
rectangular beam is selected.

Quality panel
Param. button in the quality panel
Press this button to edit the high quality definition located in the echograms control dialogs
Quality page

About rectangular beams

The SED detector can be set up to detect echoes according to a rectangle rather than to an
ellipse or circle. This may have advantages for tracking because tracks then will have the
same track length both in the center and in the outer part of the beam. Note that the
fundamental beam and its sensitivity can not be changed. This means that a rectangular
beam will have a variable sensitivity along the edges. The corners will have lowest
sensitivity and thereby lowest target detection probability. This must be considered if
rectangular beams are applied.

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Main menu

ABOUT ...................................................................................................................................................................425
SURVEY OVERVIEW ...............................................................................................................................................426
How to connect additional data .......................................................................................................................426
Where to place additional data ........................................................................................................................427
How to open additional data ............................................................................................................................427
How to open echograms at special places .......................................................................................................427
EVENTS..................................................................................................................................................................427
What is an event? .............................................................................................................................................427
Finding the ping number of an event noted at a specific time ..........................................................................428
Top menu ..........................................................................................................................................................428
Importing events from text files ........................................................................................................................428
Saving and loading events ................................................................................................................................430
Event browser page ..........................................................................................................................................430
Event editor page .............................................................................................................................................431
Start and stop events ........................................................................................................................................432
VESSEL LOG ...........................................................................................................................................................417
Apply button .....................................................................................................................................................418
Clear event button ............................................................................................................................................419
Select files button .............................................................................................................................................419
Log type selector ..............................................................................................................................................419
Distance based panel .......................................................................................................................................419
Time based panel .............................................................................................................................................419

About
There are two ways to link the acoustic data and other data files. They are the Survey map
and the event system. Both systems are accessed from SonarX’s top menu named Survey.
Events can also be opened directly from the echogram menu

Survey overview plot transects graphically in a map and indicates with graphical marks
where additional data has been recorded. The transects will indicate what you see on the
echogram, where additional data has been recorded and let you open the additional data
with the program dedicated to that kind of data, e.g a spreadsheet program,, statistical
package and so on.

Events and vessel log is a system that enables marks with associated comments to be
placed in the echograms. Marks can be vertical lines placed for example every nautical
miles starting with the first ping in the first file, or lines, boxes and free hand drawings
pointing out special events. The marks will appear automatically in the echogram and they
are listed in the event browser. Clicking a mark in the browser will bring up that part of the
echogram.

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Survey overview
The Survey overview is opened from the Survey => Overview menu. It plot transects
graphically and indicates events and where additional data has been recorded with marks in
the map. When the operator present parts of the echograms the transect maps will point out
the part seen in the echogram so that the operator always can see where the echogram has
been recorded

Figure 229 Survey map with transects and additional data. The circle indicate where the
file D20051011-T123612 Plankton sampling.xls has been recorded, and what part of the
transect that is currently seen in the echogram.

How to connect additional data

Data is connected through a date and time mark in the file name. Additional data can be
marked as point data or interval data. One time mark indicates a point while two time
marks indicate an interval.

Point : D20051011-T134100 CTD.xls

From..to : D20051011-T134100-T142300 Catch data Haul 1.xls

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Where to place additional data

The additional files are by default looked for in the same folder as the echogram. If placed
in other folders, the operator must use the folder opener in the right upper side of Figure
229 to tell the system where to find the files.

How to open additional data

Additional data files are opened simply by dbl clicking at the filename listed in one of
Figure 229’s file list boxes. If the file has an extension assosciated with a special program,
the file will be opened with that program. As an example, clicking a file with extension
.DOC or xls will cause Word or Excel to open the file if they are installed on that PC.

How to open echograms at special places

Clicking a point along transect in the Survey map will list all available echograms for that
point in the lower left list box. It may be one echogram file or it may be many if there are
multiple frequencies, multiple beams or processed levels available. Double clicking one of
the listed echograms will open the echogram at the position clicked in the map.

To open additional data elated to an echogram, click the additional data file in the right file
list box. If there are any echogram files covering that file, the plot of that transect will
change color and a circle will indicate the place where the additional data was recorded.

Events

Figure 230. Event notes in the echogram. Two event lines and two free hand drawings are
seen

What is an event?
Events are overlaid graphics, stored in separate files. The event files have the same name
as the echogram file, but with the extension: .eve or .event. When an echogram is opened,
the system automatically checks for an .eve file with the same name as the echogram file in
the same folder. If found, and if it contain any marks or events to be overlaid, found events
will be plotted on top of the echogram, when the echogram presents the correct pings. If
the echogram file is moved to another folder, the event file must be moved too. If another
person has the same echogram file, only the event file needs to be transferred to the other
person’s computer.

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Finding the ping number of an event noted at a specific time

Events occurring during recording of a sonar file will normally be noted by time and not by
ping number. To find the correct ping matching the noted time, one can move the cursor in
the echogram until the correct time is displayed in the echogram caption and then note the
ping number. An alternative is to open the echogram control dialog at the Goto page. Here,
moving the scrollbar will display matching ping and time.

Top menu
The top menu holds items for save, load, delete, help and exit. Event files can be stored or
loaded with other filenames than the default file name. This enables various sets of events
to be defined. Only the default event file will be loaded automatically when the echogram
is opened. The default event file is saved when the save menu is selected. Other event files
must be loaded with the Event-file =load menu. The Edit =Clear all menu will clear all
events from memory, but will not delete the default event file. To delete the event file on
disk, the Edit =Delete all menu can be applied. The help menu opens this chapter.

Importing events from text files

A text file with event notes or survey log can be imported and used to create for example
analysis start and stop events. The file can be created in an editor like notepad or Excel if
the Excel file is stored as a text file with tabulators separating the columns.

The format is as follows. ( Note that a vertical bar | mean tabulator sign)

; in the beginning of a row means comment and are not read by the importer
; Date | Time, | Event kind nr | Color | Line thickness | Event text
2009.10.06 | 22:00:54 | 1 | 2 | 3 | Test
2009.10.06 | 22:11:22 | 0 | 2 | 3 | Boat passage

where
Comments “;” in the beginning of a line indicates a comment not to be read by the
event handler.
Column Tabulator separates the columns. In the example above “|” represent a
separator tabulator character. Programs like Excel can save files in plain text
here the tab-character indicates the column
Date format yyyy.mm.nn is the year month and date. Dot is the separator
Time format hh:nn:ss is the time in hour minutes and seconds. Colon is the
separator
Event kind nr Number 0..13 as described in the event kind table below.
Color Color is a code from 0 to 9 where 0=black, 1=brown, 2=red, 3=orange,
4=yellow, 5=green, 6=blue, 7=violet, 8=gray and 9 is white.
Line thickness Line thickness is the number of pixels for the event line.
Text description Text is the event description that will appear in the event handler for
the event in question.

The event file is loaded from the event dialogs file menu located on the top of the dialog.

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Two menu items are available, one deals with the echogram file that is seen at the moment,
and a second deals with all files that has been selected in Sonar5’s file open menu.

Event kinds
There are currently 13 defined event kinds. The dedicated events have special meaning to
SonarX. Event start and event stop are for example used by the Analysis controller II to
find where to start and end analyzing data. Macrophyte top and bottom are other examples
of dedicated events used for special purposes by SonarX. Free events are meant for
information only, and do not have any impact on SonarX.

Nr Meaning of event kind number Event dedicated to

0 Point event Free
1 Event start Used by the analysis controller II
2 Event end Used by the analysis controller II
3 Vessel position Free
4 Time mark Free
5 Fish school Free
6 Macrophyte top Macrophyte analysis
7 Macrophyte root Macrophyte analysis
8 Fish pen Fish pen detection
9 Fish pen predator net Fish pen detection
10 Fish pen bottom Fish pen detection
11 Horizontal line Free
12 Training event Crossfilter parameter detector
13 Amp track Free

Example of use
The method was originally implemented to assist in a boat avoidance experiment in
Finland Sept. 2002. Here the echogram was recorded from an anchored vessel with the
engine turned off. A different vessel passed at noted times. Fish tracks where obtained
from periods surrounding the noted passing times and from periods without boat passages.
Then tracks influenced by the boat and tracks not influenced by the boat were compared in
the track statistic dialog found in the classification window. To help the operator to track
fish only within the correct periods, thick read event lines was added at the boat passing
times while thin green lines was added 200 ping before and after each passage. The lines
were a great support while tracking fish for the two classes.

In Malmø (Se) 2003 we studied interaction between passing trains on the Øresund bridge
and Cod. Train passage date, time, type and direction were noted in a text file. All the
recorded echogram files were opened and the log was read by the event dialog. With
hundreds of train passages during three days of recording, this option was a great help.

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Saving and loading events

Defined events are not saved automatically and the operator must select the Event-file =>
save menu to preserve defined events for later use. Events saved with the save menu will
be loaded automatically next time the echogram is opened. Alternatively, events can be
saved to other files with the Event file menu's save as menu. Events not saved with the
default name have to be loaded with the Event-file load menu. Default name is the same as
the echogram file name, but the file type is .event and not .uuu.

Event browser page

Figure 231. Event browser page

Pressing the arrow buttons presents the next or previous event. The event is presented
both in the event note dialog and in the echogram. Selecting an event number in the Jump
to event edit box will present the event in the event description panel. The echogram will
not be updated to show the event. To see the event in the echogram, the now button must
be pressed. This let the operator browse through the event list without being delayed by
echogram updating. Pressing the now button will open the echogram 50 ping before the
minimum ping described by the event in question. By clicking an event in the event list
box, that event will be presented in the echogram.

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Event editor page

Figure 232. Event description panel.

The Edit event page has components for inserting, removing and modifying events. When
an event is opened from the browse page, text and graphical presentation can be changed.
The draw button enables drawing of new events in the echogram, while the Add line button
will add a new line according to the event description.

Generating a new event

The Draw button, the Add vert. line button or the Event-file menu's Import from text file,
generate new events. The Draw button let the operator draw lines, rectangles or free hand
drawings directly in the echogram. The Add line button adds an event line at the ping
number described in the ping no. edit box. The Event-file menu enables reading event files
written in plain text. See descriptions of this later in the chapter.

Draw new button

Pressing the draw button down will set the echogram in drawing mode until the button is
let up by a repress. Click the draw button down and move the mouse into the echogram.
Press the left-mouse button down and draw the figure described in the figure panel. Then
let the mouse button up. Move the mouse to another position in the echogram and draw
another figure there. Each time the mouse button is dropped, the newly drawn figure will
be inserted into the systems internal list of events. Text, color, shape and thickness can be
set in the event description panel before or between drawing the events. Text, color, shape,
thickness, style, and ping position can be modified later.

Add vert. line button

Pressing this button will add a vertical line at the ping described by the Ping no edit box.
Text, color, thickness and style will set according to the event description panel. The line
will stretch between the echogram's min and max range.

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Ping no. edit box

Displays the ping of an existing event and let the operator specify where to add a new
event line with the Add line button.

Update button
The displayed event will be updated according to the current specifications. Text, ping no.,
color, style and thickness can be modified.

Delete no xx button
Delete the presented event number. To delete all events, use the Edit=Delete all menu.

Event no xx description
This edit box can take a short free text describing the event. The text will by default reflect
the event kind, but the operator is free write what he wants here. For example, selecting
general event in the kind selector will set the text to general event. If the operator replace
the text with “Boat passage” or “Echosounder problem” and then generates an even, the
new event will be a general event with the user applied text.

Line width
Defines the thickness of the event line, rectangle or freehand figure. Lines with a width
greater than one can only have solid style.

Line color button.

Enable selection of color for a new event or indicates the color of an existing event.

Figure panel
Determines what kind of figure the Draw button will produce.

Visible check box

Visible controls whether the event in question shall be displayed in the echogram or not.
Kind combo box
This box let the operator select among a set of predefined event kinds. There are many
different events such as a general event, a distance based log event and a training event.
Training events will be used by the system e.g. for detecting parameters from a training set.
An event marked as a vessel log event will be deleted if one deletes the vessel log.

Start and stop events

The analysis controller II can be set up to analyze periods between start and stop events in
the echograms. See the analysis controller II in chapter 7. To define Start and stop events:

a) Select “Event start” in the event kind selector.

b) Press the "Draw new" button to start the process
c) Click with the mouse in the echogram where you want the analysis to start.

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Observe that the Event kind selector switches automatically from start to stop
event.
d) Click again with the mouse in the echogram where you want the analysis to stop.
This can be in the same or in a later file. A new vertical line with a different color
will appear in the echogram, and the Event editor will again switch operation mode
and be ready for the next start event.
e) Repress the Draw new button to end the process.

The event editor will automatically switch between start and stop events. A start must be
followed by a stop. Stop events can be set in the same or in any later file. Each event is
marked in the echogram with a vertical colored line, and in the Event editors event list with
a text. Colors and text can be modified by the operator. If one click a text line in the event
editor, that event will be presented in the echogram.

Start and stop events can be imported from a text file. See the section: Importing events
from text files in this chapter.

Vessel log

A vessel log is similar to other events except that it is repeated for a defined period of time
or distance. The apply button start the measuring process from the beginning of the first
file selected in the file open menu and continues until the last selected file have been
processed. Ping numbers are calculated along the way and events are inserted each time a
new “milestone” is passed. The process ends by reopening the last viewed echogram file.

NB!

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It is important that the selected files are consecutive in time or distance for the process to
work correct. If two files containing the same time interval or distance interval are
selected, then the process may be confused. As an example, selecting a file a.uuu and the
same file, but processed a.uuuq, or a file a_ch1.uuu and a_ch2.uuu may not work well
because the system will see that the time and positions jump back and repeats when the
second file is processed.

Apply button
Generate the vessel log for the selected files.

Clear event button

Deletes old time or distance based vessel log events. Other events will not be deleted.

Select files button

Opens the file open dialog.

Log type selector

Enables selection of distance based or time based log.

Distance based panel

This panel is visible only if distance is selected in the log type selector. The panel enables
selection of distance between each log mark and the wanted log unit.

Time based panel

This panel is visible only if time is selected in the log type selector. The panel enables
setting of the time between each log mark

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Main menu

ABOUT ............................................................................................................................................................. 435

RAY AND INTENSITY PAGE ............................................................................................................................... 436
TEMP, SPEED AND ALPHA PAGE ........................................................................................................................ 437
Sound profile correction ............................................................................................................................ 438
BOTTOM PROFILE PAGE.................................................................................................................................... 439
FILES AND FORMATS ........................................................................................................................................ 440
STARTING THE SOUND PROPAGATION MODULE ................................................................................................ 440
DECIMAL SEPARATOR ...................................................................................................................................... 441
CALCULATIONS OF SOUND AND ABSORPTION COEFFICIENTS............................................................................ 441
RAY-TRACER ................................................................................................................................................... 441

About
The sound propagation module can be applied to
a) Study sound propagation from a horizontally aligned transducer.
b) Study temp, sound speed and alpha as a function of range.
c) Correct echograms by applying a dynamic sound speed and alpha profile to
echograms recorded with constant sound speed and alpha.

Access (a, b) with SonarX’s main menu: Analysis=>Pre analysis=>Sound profile

correction.
Access (c ) with SonarX’s main menu: Analysis=>Data insight =>Sound propagation
and ray-tracing.

We wrote the sound propagation module to estimate factors influencing the sound
propagation. The module calculates and plots the sound speed and absorption coefficient as
functions of depth. The module interfaces a ray-tracing module estimating “true” sound
propagation and target position. Ines Hafizovic developed the ray-tracing module as a part
of her master degree. It estimates the refraction of the sound beam caused by temperature
gradients in the water, the reflection from bottom and surface and the position of a target.
The master thesis of Morgan Kjølerbaken and Vibeke Jahr (2003) have formed the basis
for Ines’s work.

Together with Frank R Knudsen from Simrad, we observed strange sound phenomena in
River Tana (No) summer 1998, 1999. In summer 2000 we saw similar phenomena together
with Jan Kubecka in his test pond in Rimov (Cz). In River Tana, beam mapping showed
that a the target could be clearly observed all the way from bottom to surface at ranges
from 6 to more than 50 meters. The echo intensity seemed to decrease with range
according to cylindrical spreading and not like the traditionally assumed spherical
spreading. With an opening angle of 4 deg and a river depth from 2.7 at the transducer
increasing to 4 m at 50 m range this should not be possible if one consider the 4 deg

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opening angle of the transducer. The intensity of the target increased with range behaved
like In the Rimov pond, two beams were observed. One beam was observed as expected,
but under this beam, another beam was found. See (Balk, 2001 Article V11). Searching
for explanations, we have carried out hydrophone measurements in lakes and rivers and
developed sound propagation models. We have so fare not been able to explain the
observations in River Tana and Rimov, but we have learned that even small changes in the
temperature may have significant influence on the sound propagation and that reflection
and multiple paths may occur and influence strongly on the returned echo. The module
described in this chapter can be a help estimating “true” propagation of the sound beam.
Hence, a better estimate of the target position may be obtained.

Ray and intensity page

Figure 233. The ray and intensity tracing page starts the tracing. Before running the
tracer, ensure that the information on each page are correct.
Trace button
Press this button to start ray tracing.
Intensity button
Press this button to start intensity tracing.
Close button
Close the module without
Help button
Opens this document if it is available in the programs sub-folder Help_Doc
Transducer panel
The values in the transducer panel define the transducer position and opening angle. When
the module starts, tilt, depth and opening angle get their values from the open file’s
parameter dialogs. Otherwise the values will be defaults. Opening angle will athwart ship
or along ship depending on the alignment described in the application page of the dialog

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opened by the “Utility => Description of the sonar file” menu.

Target panel
This panel describes the range and the average vertical position of a tracked target.
Whether vertical position is the along or athwart ship axis is defined by the transducer
alignment. Alignment is described in the application page of the dialog opened by the
“Utility => Description of the sonar file” menu. If the “plot target” checkbox is checked,
an additional ray will be drawn trough the estimated target position. The target position
will be indicated with a rectangle.
Bottom panel
Select the bottom material or define the bottom density and the sound speed in the bottom
material directly. This information is used by the intensity tracer. It is not needed for the
ray tracer.
Surface panel
Select the surface material or define the surface density and the sound speed in the surface
material directly. In the case of ice, define the thickness. This information is used by the
intensity tracer. It is not needed for the ray tracer..

Temp, speed and alpha page

Figure 234. Sound profile page. NB this page will look slightly diifferent depending on
wether the module was started from the Analysis=>Pre-analysis menu or from the
Analysis=>Data insight menu.
Plotting a profile
To plot a profile, click the column that holds the profile to be plotted

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Environment variables
The sound speed and absorption coefficient calculations need salinity, The absorption
coefficient calculations needs also the sound frequency and pH. The sound profile
correction algorithm needs the original constant sound speed applied by the echosounder
during the survey.

Profile edit buttons

This panel has buttons for maintaining and editing the profiles. The grid holds the
temperature, sound speed, and absorption coefficient values as functions of depth. Edit the
values directly in the grid or load a profile from a file with the load button. Note that
pressing the calculate button will calculate and overwrite sound speed and absorption
coefficient columns.

Calculate speed and alpha button

This button calculates sound speed and absorption coefficients. Existing sound speed and
absorption coefficient values in the profile grid will be overwritten.
Alpha is calculated according to Francois and Garrison 1982. Sound speed is found
according to Del Grossos formula as described in Urick (1983).

Insert buttons
This button inserts an empty column to the left for the cell marked as active. An active cell
has a darker color then than other cells.
Remove buttons
This button removes the column to the left for the active cell in the grid.
Clear button
The clear button clears all entries in the grid.
Save and load buttons
These buttons enables saving and loading profiles. See the format section below.
Auto calculate checkbox
When on and when a column in the grid is clicked, sound speed and alpha will be
recalculated. If the auto calculate is on when the Sound profile correction button
is pressed, parameters such as Sound freq., sound speed, salinity, and Ph will be updated
according to each selected file before sound speed and alpha is recalculated.

Sound profile correction

When the module is opened from SonarX’s main menu: Analysis=>Pre analysis, additional
tools for correcting echograms will be visible in a separate control panel above the chart.

The correction algorithm will rearrange the Amp and SED echogram and correct range,
TVG, pulse volume, TS and Sv according to the profiles seen in the grid at the Temp,
Speed, Alpha page.

If the auto calculate is on, Parameters such as Sound freq., sound speed frequency,
salinity, and Ph will be updated according to each selected file and new sound speed and

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alpha profiles will be calculated.

When the echosounder recorded the data, it applied a constant sound speed. Based on this
speed, the echosounder estimated the distance to each target. With sound speed set higher
than the true sound speed, targets looks closer than they really are. This will influence on
the TVG.

The correction algorithm finds the assumed depth of each recorded sample according to the
applied constant sound speed. True depth is found from the integrated sound speed profile.
The ratio between the applied speed and the integrated profile is used for the correction.
The old TVG and pulse volume based on the constant sound speed and the constant alpha
is removed from all samples and single echo detections, and new samples and single echo
detections are rebuild with the correct sound speed and alpha.
Run button
This button starts the sound profile correction.
Open result files checkbox
The corrected file will be opened automatically. If multiple files were selected, the last
processed file will be opened.

Process all selected files checkbox

Multiple files can be selected in the main file open and advanced file open menu. If
multiple files ha been selected and this check is on, all the selected files will be processed.

Bottom profile page

Bottom profile panel

This panel has a grid and buttons for maintaining and editing the bottom profile. Drawing
the bottom line directly with a pencil in the position diagram in “exact display mode”

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before opening the sound propagation dialog is an alternative way to edit the bottom.
During the drawing, the position diagrams caption will indicate the pencil positions z and
depth coordinates. Note that the max range plotted by the ray-tracer is set by the right most
z-value in the bottom profile grid.

The buttons at this page does the same to the bottom as the buttons on the previous page
does to the temp, speed and alpha profiles
The red arrows lift or move the profile as much as stated in the edit box behind the arrows.

Files and formats

When calling the sound profile module, the sound, temperature, and absorption coefficient
profiles in the profile’s grid will be attempted loaded from a default file with the name
TempSpeedAlphaProfile.txt. This file will first be searched for in the working folder. If not
found here, the program looks for it in the program folder. The format is plain ascii text
with tabulators separating the columns. Hence, spreadsheets like Excel can read and write
the profile files. For the TempSpeedAlphaProfile.txt file, four columns of numbers are
expected. They are depth, temperature, sound speed, and the absorption coefficient with
depths in the first column. If the last or the two last columns are missing, reading will
result in empty cells in the profile grid. The file with the bottom profile has the same
format as the other file, but contains only two columns, depth and Z, where depth is the
vertical distance from surface, and Z is the horizontal distance along the surface.

0 10 1446.59 4.48
1 9 1442.62 4.66
2 11 1450.51 4.31
3 12 1454.33 4.15

Table 15. Example of profiles edited in a spreadsheet. From left, the columns contain
depth, temp, sound speed and absorption coefficients
Operating with sound speed and not temperature
Do not press the calculate button above temperature, sound speed, and absorption
coefficient (alpha) grid. This button calculates speed and alpha, and overwrites the values
in the table. Enter the sound speed values directly in the table’s row marked sound speed.
It is not necessary to enter temperature values. Alternatively, the table can be loaded from
a file according to
Table 15, where tabulators or space separate the numbers in each row. Dummy values like
-1 should be entered in the temperature column to indicate that they are not applied. Note
that the system always read the sound speed when executing call to the ray-tracer.

Starting the sound propagation module

The sound propagation module can be started from the position diagrams popup menu or
from the main Utility => tool menu.

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Figure 235. The ray tracing module can be started from the position diagram window’s
popup menu (left) by right clicking with mouse in the window (right). Target, tilt, opening
angle and bottom profile will be transferred to the module from the position diagram.

Decimal separator
The decimal separator is dot (.) and never comma.

Calculations of sound and absorption coefficients

Del Grossos formula as described in Urick (1983) page 113 is applied for the sound speed
calculations. The formula is valid for Temp (T), Salinity (S) and depth (D) in the range
0<T<35, 0<S<45 0<D<1000.

Francois and Garrison 1982‘s equations are applied for the absorption coefficient
calculations. This equation is also given on p 57 in Foote K.G., H.P. Knudsen, G. Vestnes,
D.N. MacLennan, E.J. Simmonds. 1987, and in. Calibration of acoustic instruments for
fish density estimation: A practical guide. ICES, Cooperative research Report, No 144,
69p.

Ray-tracer

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Figure 236. Intensity tracer written by Ines Hafizovic 2004

Figure 237. Ray-tracer written by Ines Hafizovic

Installation
The ray-tracer is a stand-alone module and not a part of Sonar5. However, if installed as
descried here the trace button in Sonar5’s sound propagation dialog will be able to open it.
The ray-tracer can be installed from SonarX’s installation CD’s released after the date
02.03.2004. It is also possible to download and install the module manually. To do so, the
zipped file named ray-tracing, including subfolders must be downloaded, unzipped and
placed as a subfolder to SonarX.exe As an example, if Sonar5_Pro.exe is located in the
folder :
C:\Balk_Lindem\Program\Sonar5_Pro.exe , then the folder
C:\Balk_Lindem\Program\raytracing\........
must exist for Sonar5 to be able to access the ray-tracer. If not, pressing the Trace button
on the sound propagation module will report that the ray-tracer is unavailable.

Meaning of the ray tracer plot

 Red line: Propagation of the sound along the acoustic axis.
 Green line: Sound path to a tracked target
 Green box: Estimated position of a tracked target
 Blue lines: Rays within the transducer’s opening angle indicating the beam
 Black line: Bottom profile

Max range
Range is here the same as z in the sound propagation dialog, indicating the distance along
the surface. The right most value in the sound propagation dialog’s bottom profile controls
the max range. If this profile ends at 18 meter, the ray-tracer estimates 18 meters as in the
example figure.

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Main menu

ABOUT ............................................................................................................................................................. 445

WHAT IS A MULTI FILE SET .............................................................................................................................. 446
HOW TO OPEN THE MULTI FREQUENCY TOOLS ................................................................................................. 446
MULTI FREQUENCY SETUP DIALOG .................................................................................................................. 447
OPENING MULTI FREQUENCY FILES .................................................................................................................. 447
OPENING FILES FROM DIFFERENT PARTS OF A SURVEY..................................................................................... 448
SYNCHRONIZING ECHOGRAMS ......................................................................................................................... 448
STUDY THE FREQUENCY RESPONSE .................................................................................................................. 448
FREQUENCY RESPONSE CONTROL DIALOG ....................................................................................................... 449
RGB-ECHOGRAMS ........................................................................................................................................... 450
CLASSIFICATION MAP ...................................................................................................................................... 451
FREQUENCY RESPONSE FUNCTION ................................................................................................................... 452
Exporting frequency responses .................................................................................................................. 454
DIFFERENTIAL ECHOGRAMS ............................................................................................................................ 454
FREQUENCY RESPONSE THRESHOLDING ........................................................................................................... 455
MASKING UNWANTED TARGETS AND NOISE ..................................................................................................... 457
ADD FREQ. OR CHANNEL TO A MULTIPLE FILE SET ........................................................................................... 459

About
The intensity of echoes from targets depends on the targets acoustic density relative to the
water, size, orientation, and echosounder frequency. Studying the frequency response from
different targets can give important information about what the targets are. The frequency
response can help separating bottom with and without corals, fish with swim bladder from
fish without swim bladder, fish from plankton and one plankton species from another. This
has been reported in the literature.

Sonar5 can give visual and quantitative insight in the frequency response. Multiple
echograms can be set up to show the echoes from the different frequencies simultaneously.
All echograms can be synchronized. Individual echograms can also be released from the
synchronizing. This allows the operator to study and compare different echograms at the
same time and different events at different times. When synchronized, operations such as
moving around or zooming will operate on all echograms. If one echogram is asked to
show data from a special ping number, all the other echograms will do the same.
Biomass estimation will be carried out on the echogram that asked for the estimate, but the
biomass window has a list of available frequencies and selecting another frequency will
show the estimate for that frequency. For classification of targets, frequency response
functions, frequency response maps and RGB echograms are available. Echograms with
different frequencies can also be subtracted or one echogram can be applied as a mask to
another.

Multi frequency tools are found in

 the top menu named Multi freq.
 a section in the Echogram menu, (Clone echogram , Frequency selection and File
open)

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 the Analysis => Data insight menu (Frequency response and RGB-echogram)

What is a multi file set

A multi file set is a set of files you want the system to load simultaneously. In practice it is
a set of files with a channel indicator in the file name. This mechanism was originally
intended for multi frequency analysis, but there are situations where one wants to combine
simultaneously recorded files with equal frequencies as well.

Example:
MyFile .UUU is a stand alone file while
MyFile_CH01.UUU is part of the MyFile set.
MyFile_CH02.UUU is also part of the MyFile set.

When you open a file with a channel indicator, Sonar5 will look for all available files with
the same name, but with different channel indicators. All will be loaded. Many operations
work on multiple files such as the frequency response function, integrating the echoes
within the selected region for each channel to plot the response.
Normally multi channel files come directly from the echosounder if for example
two frequencies or more have been applied during the recording. If so, the converter will
set up and name the different files automatically.
It is, however, possible to build up multi file sets from different echo sounders with the
menu “Add freq. to a multiple file set”. (See description later in this chapter.)

How to open the multi frequency tools

Tools related to multi frequency analysis are located in the top folder named Multifreq.

Figure 238. Multi frequency menu

The Setup will open a setup template from where one can select various fixed setups. As
an alternative to using the pre made setups, one can open analysis windows such as the
RGB echogram and the frequency response function window directly.

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Multi frequency setup dialog

Figure 239. Multi frequency setup dialog

The multi frequency setup dialog is accessed from the systems top Multifreq. menu. Here
one can select a number of echograms to be seen on the screen together with additional
tools such as biomass, frequency response, image analysis and tracking tools. The
echograms will be distributed on the screen either with equal size or with one large and
many small echograms depending on the setting of the Echogram size selection.

Opening multi frequency files

When a source file that contains more than one channel is converted, the file will be split
into one converted file for each channel. When one of these files is selected in Sonar5’s
File=>Open menu, the selected channel will be loaded into the echogram. If more than
one echogram window is open at the time a file is loaded, the available channels will be
distributed and presented in the different echograms as far as there are enough echogram
windows available. Each echogram has a popup menu (accessed by a right mouse click)
with a Frequency selection item. This menu can be used to change frequency. Frequency
can also be changed with the short key Ctrl+1 for channel 1, Ctrl+2 for channel 2 and so
on. See the top menu: File=>Quick file open for changing channels and processing stages.

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Using Channel filters

The File => Advanced file open dialog has filters that can prevent showing all the channels
for each file when one want to open files for conversion. Use the channel selector to see
All Channels or individual channels listed in the file open list box.

Opening files from different parts of a survey

Start by opening another echogram window. This can be done by selecting a new
echogram from the Analysis =>data insight =>Echogram menu. Then right click with the
mouse in the new echogram and select File open from the appearing popup menu. This
enables selecting a different file for the echogram than currently presented in the other
echograms. Being able to study many echograms at a time can be a help e.g. for comparing
echo phenomena and biomass from different fish schools etc.

Synchronizing echograms
Each echogram has a control dialog. Clicking on the echograms color, depth or ping bar
opens the control dialog. If the Apply to all check box is checked, operations such as goto
ping, change threshold, zoom, etc. will influence on all opened echograms. The Apply to
all check box located below the Apply button in the upper left part of the echogram control
dialog

Study the frequency response

A specialized window with a separate control dialog has been designed to give insight in
the response. The control dialog is seen in Figure 240. The control dialog can set up the
frequency response windows in various ways, align the transducers in time and range, set
up what frequencies to apply for each color and define filter coefficients. Many frequency
response windows can be opened at a time if one wants to see different results
simultaneously. E.g an RGB echogram, a response map and a response function. Each
response window has its own control dialog. The look of the dialog will change when
different options are selected.

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Frequency response control dialog

The frequency response control dialog controls the frequency response windows. Each
response window has its own control dialog, thus, different response windows can be set
up to display different aspects of the data at a time.

Figure 240. Frequency response control dialog controls the response window.
Option selector
The selector defines how the frequency response window shall present the frequency
response. The meaning of the RGB options is explained in the RGB echogram section, the
meaning of the classification map option in the classification map section and so on.
Frequency selector
The frequency selector enables the operator to select what frequency to connect to which
color. Clicking the arrow down in the frequency combo boxes gives a list of the available
frequencies.
On/off
The on of check boxes opens or blocks the color in question. The check box behind the red
color blocs the red color and so on. This is useful both for trimming the ping and range
displacement and when one want to focus on the response between two particular
frequencies.
Focus control
The transducers cannot be mounted at the same position, thus, the beams will not overlap
when the ship is moving. This results in a picture looking slightly out of focus. If the 38
kHz is places in front of the other transducers and connected to the red channel, fish tracks
will look red in the front and blue or green in the end depending on the frequency and color
of the last mounted transducer. If any of the transducers are responding slower or faster
than the others, range displacement will be the result.

The ping and range scroll bars or the edit boxes behind the scrollbars can move the green
and blue beam in range and time. Select an area in the echogram with the mouse
containing a few clear tracks, turn off the blue color channel with the on/of checkbox and
adjust the green channels displacement until the tracks overlap the red track. Repeat the

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process for the blue color channel. Try different filter sizes and options to find a view that
makes it easy to see how well the beams overlap.

Interpolation is applied to enable the displacement controls to move the data in steps down
to 0.001 pings.

RGB-echograms
The human eye detects three colors, red, green and blue. A color monitors have three color
cathodes or channels matching the same colors. When the monitor supply the same energy
to each channel, colors from black through gray to white will be seen. If the amount of
energy is varied, all colors can be generated.

What is then more natural than presenting the echo intensity recorded with three
frequencies as intensity in each of the monitors color channels. A target with decreasing
frequency response will look red while targets with increasing frequency response will turn
blue. This is what the RGB echogram does. Figure 241 gives an example. See also
Cochrane et. al.(1991)

Figure 241. Example of an RGB-echogram

RGB echogram can be opened directly from the multi freq menu. Alternatively an already
opened freq response window can be changed to another kind with the control dialogs
option panel. Press the control button seen in the top panel of the frequency response
window and select one of the RGB options in the option panel.

What is a RGB echogram?

Each color on a LCD or TFT monitor can take integer intensity values from 0..255. Sv or

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TS can take on any real values from at least -100 dB up to at least 0 dB. This is the
dynamic range of the echosounder. Sv or TS values must be mapped so that the weakest
echo maps to 0 while the strongest must not exceed 255. The dynamic range can be
mapped in various ways to produce the RGB echogram. The mapped values we can be
multiplied with the contrast and added the brightness value to obtain a RGB-echogram that
highlight what we want to study.

The RGB echogram has four options, which can be selected in the control dialogs option
panel. The options are
RGB scaled to max
The RGB colors are produced by first scaling so that the echogram threshold is mapped to
0 and the maximum possible Sv or TS value are mapped to 255. The mapped values are
multiplied with the value given by the control dialogs contrast edit box and added the value
of the control dialogs brightness edit box. The contrast and brightness may cause the
resulting value to exceed the color span. If the overflow protection is on, values below 0
are set to 0 and values above 255 are set to 255.
RGB scaled to measured
Same as for option 1, but in stead of scaling to the total dynamic range, the dynamic range
found within the analyzed region is applied. This will automatically increase the contrast in
areas with low difference in the frequency response.
RGB no scaling
The Sv or TS samples from the Amp echogram are simply multiplied with the contrast and
added the brightness.
RGB differential
Red channel is assigned to the constant brightness plus 128. Green and blue are found as
the difference towards the constant red value. The differences are multiplied with the
contrast.

Classification map

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Figure 242. Frequency responce window set up to present the classification map. The
colors and the resulting percentage of each color is reported in the control dialogs
classification panel.

Figure 243. The control dialogs classification panel with the color rules and the resulting
percentages for an analysis.

When the option 5:- classification map, is selected in the control dialog, the color
adjustment panel is replaced with the classification panel. This panel presents a set of rules
connected with different colors. When a region in the amp echogram is analyzed, the
frequency response window will take on the different colors according to the rules. The
percentage of samples responding to each rule is presented behind the color rules in the
control dialog.
Threshold
A difference threshold can be set to give regions with insignificant difference a separate
color.
Colors
The mapping colors can be changed by clicking the individual color rule bar with the
mouse. As an example, clicking for the 1>2>3 bar will open a color selector dialog where
a different color can be selected. The system will store the selection in the default
Sonar.cfg file and apply the selected colors next time the system is started. If the frequency
response window is closed before sonar5 is closed, changes will not be remembered.

Frequency response function

The frequency response function does echo integration for all available frequencies in the
selected echogram region and presents the result as a function of frequency. Sv and sA
from the Amp echogram and TS from single eco detections can be integrated.

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Figure 244. The frequency responcewindow set up to present the Sv responce for a three
frequency survey.

Figure 245. Control dialogs responce function panel. The panel is only visible when the
frequency responce function option is selected.

Show selector
This selector controls whether Sv, sA or TSc or TSu shall be presented. When Sv or sA are
presented, the echo integration is performed on the data from the Amp-echogram. When
TSc or TSu is selected, TS values from the single echo detections in the SED-echogram are
averaged and presented. subscript c means off-axis compensated while u indicate not
compensated.
sA unit selector
This selector controls the units for the reported sA.

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Exporting frequency responses

Figure 246. Bottom part of the frequency response control dialog logs the results from the
analysis. This data can be exported.
In addition to presenting the frequency response graphically, the background data is
available in the frequency response control dialog from where they can be exported in
tabulated form to clipboard.

The data that can be exported is: Filename, Frequency (kHz), analyzed region, (ping,
range)
Mean Sv (dB), Mean sA, Mean TSc (dB), Nr of Amp samples, Nr of SED, sv/ts ratio,
Sawada index, Averaging method. The sv/ts parameter is found from the linearized Sv and
TSc values. It can be interpreted as the abundance of targets per m3 for a one size class
analysis using the echogram thresholds to define the lower end of the size class. Sawada
Index is also found from this one size class analysis. Be aware that a one size class analysis
is extremely crude and that the values found here normally will differ a bit from the output
from the multi size class analysis carried out by the biomass estimation tools.

Differential echograms
One echogram with data from one channel or frequency can be subtracted from another
echogram with another frequency. This enables the operator to create a differential. For
example if herring and mackerel schools are present in 38 and 200 kHz echograms, the
herring is supposed to have higher echo intensity than the mackerel at the low frequency. It
is then possible to generate a new echogram that contains the difference. All available tools
in Sonar5 can then be applied to study the difference. The 3D-Echogram can for example
be applied to study the intensity or the higher order statistics of the difference. The
echogram can be thresholded and regions with high difference can be applied to mask the
original echograms.

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Figure 247. Subtracting one echogram recorded with one frequency from another
echogram with another frequency will generate a differential echogram.
See the explanation under Figure 248 for a description of the items in this dialog.
Individual samples i,j in the new echogram are calculated according to the following
equation

 Sv(i, j ) fA Sv(i , j ) fB  
  
Sv(i, j ) diff  10  log 10 10  10 10   Factor  const 
 
 
 
where fA indicates frequency A and fB indicates frequency B. For constant not to influence
on the result, it must be set to a very low value such as -900dB. Negative differences will
then fall below the echogram threshold and not be seen. To see both negative and positive
differences, set the const value to e.g. -50 dB. Then -50 db in the result echogram will
indicate no differences.

Frequency response thresholding

The top menu: MultiFreq=> Frequency response thresholding opens this tool. The dialog
writes and executes a set of commands in the tracker windows image analysis command
editor.

The idea here is that a set of rules based on the frequency response is used to threshold an
echogram. This enables the operator to create a new echogram where all echoes that has a
higher or lower intensity, is removed. For example if herring and mackerel schools are
present in 38 an 200 kHz echograms, the herring is supposed to have higher echo intensity
than the mackerel at the low frequency. It is then possible to generate a new echogram
where either the mackerel or the herring has been removed. Biomass estimation can then
be carried out on the new echogram. The Run or test buttons generates a mask based on the
selected rule. This mask is applied to the output echogram. The dialog uses the image
analysis command MFclass2Freq. The command is described in the manual chapter 15

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Figure 248. Dialog for applying the echo intensity from one echogram as a threshold for
another echogram. Using frequency response rules may supress certain species and
produce a new echogram where one can carry out species dependent analysis.

Test button
Press the test button to see how the default parameter setting performs (a temporary
echogram is created)
Run button
Press the run button start the process indicated at in the caption and by the step 3 page. The
process will vary from single echo detection to tracking depending on from where the
dialog was opened. If it was opened from the Anlaysis => Preanalysis => SED menu the
dialog will indicate that SD will take place. If opened from the Analyze => Setup =>
Tracking => Crossfilter tracking, Tracking will take place, and so on.
Generate commands Checkbox
If checked no actual process will take place, but the commands for the process will be
written to the trackers image page. Here they can be edited further to create methods not
creatable with the templates.
Process all selected files
If checked the process will process not only the echogram file opened at the moment but
all the files that was selected in the file open dialogs.
Open result file checkbox
If checked the dialog will open the resulting file after the new file has been generated.
Action panel
This panel control how echo samples will be removed. Threshold means that the samples
are not removed but that they will be allocated extremely week Sv values far below the
base threshold. Erase means that the samples are totally removed from the echogram.

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Thresholded echo samples can be visualized by allocating a recognizable color to the

threshold level. By default this is white. See the echogram control dialogs Threshold page.
Thresholded echoes cannot be restored. Erased echoes can be restored or given
recognizable colors with the tools found in the echogram control dialogs noise page. See
also the Utilities=> system configuration dialog for more about the difference and usage of
thresholded and erased echoes.
Frequency edit boxes
Type the frequency wanted for the operation here.
Filter height and width
Height and width indicate the number of samples in the range and ping domain
respectively, included in a running mean filter smoothing the echogram
Offset
The offset value is added to all samples in the echogram with the frequency noted in the
frequency-A panel.

Masking unwanted targets and noise

The masking dialog is found in the top menu: Multi frequency =>Masking

A mask is simply an echogram where something has been erased. Masking is a process
where one erases unwanted echoes in one echogram and uses that echogram as a mask for
echograms with other channels or frequencies. In plankton studies, fish are noise and can
be erased manually or automatically. Since fish are best detected in the lower frequencies,
one can erase the fish there and let the masking algorithm use that echogram as a mask for
all the other echograms with higher frequencies. The masking dialog is designed to work
on multi-channel file sets.
How to make a mask
A mask can be made manually by pressing the “Manually” button and using the appearing
Erase and Recall tools. Masks can also be made automatically by pressing the Automatic
button that opens Crossfilter detector tuned for noise reduction. An automatically detected

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mask can be manually modified before it is used to mask the other channels.

How to use the Mask dialog

Ensure that the echogram that has been prepared as a mask* is opened and listed in the
Mask dialogs notepad. If not listed, click the echogram caption to force the system to list
that echogram as the mask. Type in the channel numbers or the frequencies you want the
mask to be applied to in the dialogs “Items to be masked” edit box. Check on the correct
unit (kHz or Channel nr), and press the Start button.

* Use mask from higher processing level check box

If the echogram prepared as a mask has a higher processing level than the files in the file
set you want to mask, then you must check on the “Use mask from higher processing
level”.

Example 1
We assume that we have three channels in processing level 0, that targets have been erased
in echogram_ch01.uuu and that this echogram is presented the activated echogram
window.

echogram_ch01.uuu, 38kHz The mask

echogram_ch02.uuu, 120kHz Listed as a target for the masking
echogram_ch03.uuu, 200kHz Listed as a target for the masking
Pressing the Run button will now use echogram_ch01.uuu as a mask for the two others

Example 2
We assume that we have three channels in processing level 0, but that we this time have
the mask prepared in a file named echogram_ch01.uuuQ for example by the automatic
routine. Now it is important that the echogram_ch01.uuu is opened and that this echogram
is the last activated echogram. For this to work one must tell the system to take the mask
from the higher processing level by checking on the “Use mask from higher processing
level” check box

echogram_ch01.uuuQ, 38kHz The mask

echogram_ch01.uuu, 38kHz Listed as a target for the masking and activated
echogram_ch02.uuu, 120kHz Listed as a target for the masking
echogram_ch03.uuu, 200kHz Listed as a target for the masking
Pressing the Run button will now use echogram_ch01.uuuQ as a mask for the three others.

Example 3
We assume that we have three channels in processing level 0 and that we have used the
Automatic method to create a mask but that we also had checked on the automatic
detectors "Apply to all frequencies" check box when the detector was run. With this
checkbox on, the detector does the following
Input file Operation Output file
echogram_ch01.uuu Detect and erase targets to create a mask echogram_ch01.uuuQ
echogram_ch02.uuu Apply the mask from ch01 echogram_ch02.uuuQ
echogram_ch03.uuu Apply the mask from ch01 echogram_ch03.uuuQ

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If the mask is well detected one do not have to do anything more. If not one can open the
processed level (uuuQ), manually modify the masked echogram_ch01.uuuq and use this to
re-mask the two other channels as done in example 1 but with all files having the same but
a higher processing level.

Output
The echogram frequencies or channels listed in the ”Items to be masked” edit box will get
the same samples erased as those samples marked as erased in the source mask echogram.

Important to know
a) Echoes below the Base threshold do not exist, and can thereby not be erased.
Hence to use masking it is advisable to set the base threshold below the noise level
(e.g. -140 dB) to get the best masking results. Base threshold is set during
Conversion in the Initial parameters Amp page. (File=>Convert=>Initial
Parameters=> Amp )
b) If two or more echograms are present on the screen, the last activated echogram
will be the one that is used as a mask.

Add freq. or channel to a multiple file set

This method applies when you have recorded additional echograms with another
echosounder. Let us for example say that you have an EY500 operating with 70kHz
frequency and an EK60 sounder with a 200kHz transducer. The two can be run in parallel,
but they will output individual files. These files will probably start and stop at different
times and they may run with different ping rate. To utilize Sonar5’s multi frequency tools
you can build a multi-channel session from the two files. You select one file as the master,
eg the raw file from the EK60. Then you tell the system about the files from the EY500.
When you press the Run button the program will take the first ping from the source file
and look for the matching ping in the list of EY500 files. Each time a ping match within
the accepted variation, that ping will be added to the second channel file. If no matching
pings are found for a ping from the EK60, then that ping will be stored as an empty ping
with echo energy below the base threshold.

Still as an example you start with

D20100101_T105500.uuu This is the source file with 200kHz data

You pick from

10511801.DG01
11100314.DG01
11450314.DG01

The result will be two files with the following names

D20100101_T105500_CH01.uuu coming from the EK60 uuu file containing 200kHz

data
D20100101_T105500_CH02.uuu coming from the EY500 file containing 70 kHz data

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The two files will have matching number of pings and they will start and stop
simultaneously. The system will handle them as a multi file project and be able to apply
multichannel and multi frequency analysis and to show both files simultaneously and
synchronized.

Warning: If the files from the EK and the EY echo sounders have been recorded on PC’s
with un-synchronized clocks, or with systems set up for different time zones, then one
must correct the time stamps in one of the file set before running the Add freq. routine.
Changing the timing of a file can be done with the Utilities=>tools=>time adjustment
menu.

How to do it
Step 1, select master file
Ensure that the file you want to add a new channel to is selected in the edit box marked as
step1. If this file is a standalone file, the system will rename it automatically and allocate a
channel indicator to it.
Step 2, select files to pick pings from
Use the upper left File selector button to select files to pick data from. You can select many
files here. You should select files so that the selection cover the time period of the file
selected in step 1.
Step 3, run
Press the Run button in the top panel. The system will then check and if necessary rename
the file selected in step 1. Then the routine will search trough all the selected files at step 2
and for each ping in the step1 file extract the ping that are closest in time from the step2
files.
If no ping is found within the time frame given by the time frame parameter edit box, an
empty ping is added. Time periods not available in the step2 files will also contain empty
pings.
Output
The output will be a new file with the same name as the master file but with a channel
indicator different from all other channels. The chanel indicators will be sorted so that the
resulting file set will have increasing frequency with increasing channel number.
List timing check box
The list timing check box will show how well pings have been matched.
Time frame edit box
The time frame edit box let you set the accepted time jitter before an empty ping is added
to the new file set. The time frame is given relative to the time interval in the master file. If
the time interval in the master file is 1 sec and the time frame is set to 0.5, a ping will be
accepted within the master ping time +/- 1sec. If the master ping was emitted at 23:20:05
then a ping will be accepted from [23:20:04 .. 23:20:06] If there are more than one ping
within the time frame, the closest in time will be preferred.

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Main menu

ABOUT ............................................................................................................................................................ 463

TERMINOLOGY ................................................................................................................................................ 463
ANALYSIS STARTS WITH THE ECHOGRAM ........................................................................................................ 464
CONVERTING FILES INTO ECHOGRAMS ............................................................................................................ 465
DIDSON VIEWER ........................................................................................................................................... 466
DIDSON CONTROL DIALOG ............................................................................................................................ 466
MARKERS........................................................................................................................................................ 468
MANUAL METHODS ......................................................................................................................................... 468
Manual tracking ........................................................................................................................................ 468
Four ways to track fish manually .............................................................................................................. 469
Depth by shadows ...................................................................................................................................... 472
Editing tracks ............................................................................................................................................ 472
Ruler for fish sizing ................................................................................................................................... 473
Intelligent ruler.......................................................................................................................................... 474
Measuring tail beat frequency ................................................................................................................... 475
AUTOMATIC METHODS .................................................................................................................................... 476
Automatic tracking .................................................................................................................................... 476
Singe echo detection .................................................................................................................................. 477
PRODUCING AND EXPORTING TRACK INFORMATION ........................................................................................ 477

About
The DIDSON sonar is a high frequency sonar that can produce video like underwater films.
The high frequency causes reflections from the skin and fins of the fish and not only from the
swim bladder. Sonar5 handles the DIDSON files similar to any other echo sounder file. First
the file has to be converted into ordinary echograms. Events seen in this echogram can be
studied and tracked in the same way as echograms from other echo sounders. To see the
movie, set up the system for DISON work with the menu selection: Analysis => Setup =>
DIDSON. Draw a rectangle around an event in the echogram will load that part of the
echogram into the viewer where the DIDSON pictures and movie can be studied. Processing
include background subtraction, automatic tracing and classification or single echo detection.
Manual tracking, track editing and fish length ruling is also available.

Terminology
Single echo: An echo from one target seen either in the echogram or in the frame viewer. In
the frame viewer, a single echo will normally come from more than one beam and may be
seen as a picture of a fish. We still call this an echo, to be in line with traditional echo sounder
terminology.
Trace: A trace is the footprint of the fish as seen in the amplitude echogram. The banana
shaped echoes seen in vertical mobile surveys are traces. The picture of a fish in the viewer
seen in successive frames, form a trace in the echogram.
Track: A track is a series of connected single echo observations.
Ping or frame: A frame is the picture created from one burst of beams. Here we will call
such a burst for a ping. We use ping, ping rate and number of ping in a file when describing
the bursts, burst frequency, and total number of bursts in a file. In a few situations it is

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necessary to discuss the individual beam emissions in a burst. In these cases we will specify
that we talk about the individual emissions that build up the burst or ping.

Figure 249. DIDSON viewer (right) showing migrating Salmon in Kenai River recorded by
Debby Burwen for Alaska Department of Fisheries and Game (ADFG). The file is available
on the Sonar5 CD’s demo file folder.

Hints and tricks

Zooming.
Click the DIDSON viewers Menu button and select control, then:
Zooming in range. Select the range page. The options let you select whether to adapt to the
range selected in the echogram or to apply a separate range in the DIDSON viewer.
Zooming in width: Select the Frames and Beams page, and adjust the Beam presentation
angle factor.

Player speed
Normal playing: Click the DIDSON viewers Menu button and select control and then select
frames and beams. Here you can adjust the player speed. Note that this speed is overruled by
the speed in the Processor is checked on in the dialogs Auto page.
Processed playing: When the processor is checked on, the speed is controlled by the
processor independent of the setting in the dialogs control page. The speed bar on the auto
page is set to the fastest playing by default (scrollbar to the left side) For a very powerful PC
this may be too fast and one may like to reduce the speed to be able to see the fish passing.
For a not so fast PC it may not be possible to see any effect of the speed control at all because
the pc play the file slower than the slowest possible setting anyway. However if one check
on the show checkbox in the block named “4-Evaluator” and turn all other show checkboxes
off, then even a slow PC may play too fast, and one would like to reduce the playing speed
with the speed bar.

Analysis starts with the echogram

See the section “Converting files” below about generating echograms. Ordinary echograms
provide a much better overview of the recorded data than the multi beam data viewer does.

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One can look through large amount of data and obtain interesting events in a fraction of the
time it would take to play the movies. The simplest “how to do” list is as follows
1. Convert the DIDSON ddf file into an echogram
2. Setup the system with the menu: Analysis=>Setup=>DIDSON
3. In the echogram, select the region you want to study by
a. drawing a rectangle with the mouse,
b. the echogram menu: “Analyse all file”,
c. the DIDSON control dialogs “Select all” button located in the left control
column,
d. the echogram control dialogs analysis page.
4. Press the play button in the Viewer, use the tracker, turn on the auto detection system
etc.

Converting files into echograms

The converter compresses the information from the many DIDSON beams in to one beam
which is used to generate the echogram. Tools such as 3D- echograms, oscilloscopes, tracking
and classification work on these echograms.

The converter can be set up to convert the data into echograms with different opening angles
and different processing techniques. At one conversion, up to three different echograms can
be generated. These echograms can either be similar to ordinary Amp echograms containing
average intensity within the selected beam angle, or they can be Max Intensity (MI)
echograms.

For Average echograms, narrow opening angles will improve the signal to noise ratio, but
make traces from passing fish shorter. A useful setup for fish counting is to split the beam into
three echograms, one narrow centre echogram for counting, and two wider from the down and
upstream part of the beam to indicate approaching fish. MI echograms perform best when all
or most of the available opening angle are included.

Figure 250 The central part of the converter dialog. When DIDSON is selected in panel 1, the
DIDSON option panel becomes visible. See chapter 5 for description of the rest of the
converter dialog.

Setting up the converter

Select DIDSON .DDF format to see panel 1c. Then Select whether to produce 40logR or

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20logR echograms. 40 log is normally the appropriate choice. If you are uncertain about this,
select always 40. Channel nr. will be added to the resulting echogram filename and enable
multiple conversions of the same DDF file into different kinds echograms. This can be useful
if one want to extract different part of the beam or if one want to test and compare echograms
extracted in different ways. If phase file is checked on, a separate file with the extension
“.phase” will be produced. This file contains angles detected for targets in the beam. These
angles can be displayed in the echograms and used in various analysis.

DIDSON viewer
The DIDSON viewer is seen to the right in Figure 249. It can show DIDSON pictures and
movies for the pings and range selected in the echogram. It has a top control panel with a
menu button, a ping slider and a set of movie control buttons.

Figure 251. DIDSON viewers top panel

After a region is selected in the echogram, sliding the scrollbar or pressing the arrows on each
side will step or move to frames within the selected pings. Pressing the play button will start
or stop the movie playing. The Menu button has items for Help and for opening the viewer’s
control dialog at different pages. The control dialog controls setup, background subtraction,
tracking etc. See the description of the control dialog for information of this dialog. The menu
does also provide short keys witch are important for fast operation of tasks like tracking and
tack editing.

DIDSON control dialog

The control dialog has four main tabulated pages named: Control, Auto, Manual and Status.
At the left side of the controller, there is a control column with speed buttons and check
boxes.

Figure 1. Sonar5 set up to with a DIDSON echogram (left) and a DIDSON multi beam
viewer (right)

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Figure 252. Sonar5’s DIDSON viewer control dialog.

Left side control panel

Apply button
will apply the selected settings when necessary. Some controls will be applied immediately.
Play button.
The button will take on different names according to the setup and system status. Play
indicates start playing. When the control dialog is set up for auto tracking the button will
indicate this by taking the name Tracking. A third alternative is SED, which will start the
generation of a new SED echogram
Step button
The step buttons let you step forwards or backwards in the selected number of pings.
Select all button
Pressing this button will select all pings and ranges in the open echogram, and load the region
into the viewer for playing or analysis.
Close button
Close the control dialog
Auto play check box
When checked the viewer will start the playing as directly when a new region is selected in
the echogram
Multiple files check box
When checked all files selected in the file open dialog will be played or tracked, one after the
other.
Pop up check box
Not used yet
Stay on top check box
Force the DIDSONS control dialog to stay on top of other windows.

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Markers
Sonar5-Pro has a grapic overlay system enabling various graphics to be placed ontop of the
DIDSON frames. This overlay system is controlled in the Graphic overlay page.

Figure 253. Marker options.

Look up and mark stored tracks

To be able to see stored tracks, ensure that the Look up and mark stored tracks is checked on.
This will look up stored tracks and present them in the viewer when the viewer presents the
correct frame. The echogram has a similar selector in the Echogram control dialogs marker
page. This must be on for the system to look up tracks in the echogram.
Presenting detections
When a track is detected e.g with the automatic tracker or the intelligent ruler, the detection
can be presented in various ways selected in the Presentation panel. All options are available
during the detection process while some will not be seen for replay or presentation of tracks
stored in fish baskets even if selected.

Manual methods
The main manual methods are tracking, editing, and ruling. In addition, tail beat frequency
measuring is available in the Viewers menu.

Manual tracking
To track targets, set up Sonar 5 for DIDSON work with the Analysis=>Setup=>DIDSON
menu. This will provide a screen with an echogram, a DIDSON viewer, The DIDSON control
with the DIDSON tracker, a SED tracker and a classification window. The SED tracker and
the classification window are described in chapter 12 and chapter 13.

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Figure 254 The DIDSON tracker is located in the DIDSON control dialogs Manual page. It is
accessed by pressing the DIDSON viewers menu button and selection Manual tracking.
New track button
Press the “New track” button down to start the tracking process. Observe that it will change
name to Store track and that two new buttons will appear. As long as the button is down, the
system expects you to mark fish in the viewer with the mouse. The two appearing buttons can
delete the last added echo and cancel the tracking. The last button in the row will take the last
stored track out of its basket and through it in the garbage basket.

Figure 255 When the New track button is pressed, it changes name to Store track and buttons
for deleting the last added echo and for cancel tracking appear.

Four ways to track fish manually

There are four different ways to track fish

Tracking method 1: Tracking in the DIDSON viewer

This is the most accurate tracking method and gives the fish length in addition to the position
in the beam. Various options for how to do the tracking is available. For line and rectangle
tracking the “intelligent” ruler can be used. This helps the operator to find the length of the
target. To assess the targets depth, use the “Depth by shadow” check box. When the Depth
by shadows is on, the system expects a click on the shadow after each time a fish picture has
been marked.

The main principle for manual tracking is that one start a new track by pressing the New
track button down when a new fish are seen entering the beam. The New track button change
name into “Store track”, and the systems wait for the operator to mark the track in the viewer.
After the track has been marking, the system will advance one frame forward by default. NB!
note that the mark will disappear when the next frame is appearing since the mark is related to

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the frame where it has been placed. The “Advance frame after” edit box (Figure 254) controls
the advancing function. The operator can set the value freely. If set to zero, the advancing
will stop and the last track mark will be seen. Continue to track the fish along its path until it
disappears from the beam, then press the Store track button. The track will be sent out to all
opened tools in Sonar5-Pro and the tracking control button will shift name back to “New
track” ready for a new tracing process.

Do it like this
Select drawing method in the Manual trackers panel named “Drawing tool”. Read the section
about speeding up the manual tracking. Then do the following:

1. Press the New track button down (Figure 254). When pressed, the buttons title
changes to Store track.
2. In the Viewer, mark the picture of the fish with the mouse.
3. Step forwards to the next frame and continue to mark the fish until the fish leaves the
beam.
4. Repress the button that started the tracking, that was named New track in Figure 254
and that now is named Store track. This will save the track in the fish basket.

Speeding up manual tracking

No need to track all frames:
One does not need to track each individual frame echo. It is sufficient to track the first and
last observation. The system will then estimate the intermediate frame echoes. If the fish
change direction it may be good to track more than two frame echoes.
Automatic skipping frames:
In the DIDSON control dialogs Manual tracking panel, increase the “Advance 1 frame after”
to a larger number. This will automatically advance the selected number of frames after each
line has been drawn. If Advance=0 frames will not advance. If set to negative values, frames
will advance backwards.
Do everything in the Viewer.
It is time consuming to move the mouse between the control dialog and the viewer. The
following short keys can help speeding up the process. Before starting to track with the short
key’s it may be necessary to click on the DIDSON Viewers frame scrollbar at the top and left
of the Viewer’s Menu button.

Space bar = “New track / Store track” button

A-key = “Step ” button
Alt+A- key = “Step ” button

Jump back
If the Jump back function is checked on, the tracker will bring the viewer back to the frame
where the previous track started. This is useful in situation with more than one fish in the
beam simultaneously.

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Interpolation of tracks
It is not necessary to track the fish in each frame. As an example, if a fish is tracked in
frame 10 and 13, the system will guess the size and position for the track in frame 11 and 12
by interpolation. Hence, if the track is replayed one will see the track in each frame from it
enters until it leaves the beam.

Background subtraction
Background subtraction can be turned on to make it easier to see the tracks during manual
tracking. Background subtraction is controlled on the control dialogs Auto page (Figure 259).
To combine background subtraction with manual tracking, turn on the processing in the
control dialogs auto page and check on the show check box either in the 3-Comparator or 4-
Evaluator. Then open the manual page again to continue tracking with background subtracted.

Track quality system

DISON has higher sensitivity in the center of the beam and produce more accurate length
estimates here. Depending on the fish aspect and swimming motions, the fish can be better
presented in some frames than in other frames. If one wants the resulting average length
estimated from the tracked fish to be calculated only from the frames where the fish is well
seen, one can enable the Quality system. It is then important that the quality stamp is used
during the tracking by selecting either low or high in the following panel during the tracking.

If the echoes in the tracks have been marked in this way, checking on the track quality check
box in the system configuration dialog will enable this option. See the “Single echo quality”
panel in the main menu: Application=>System=>General page

Manual tracking method 2: Click tracking

Checking on the Click tracking check box set the tracker up for click tracking. The method is
designed for high density situations where one want to count the number of fish milling
around in the beam. Each click will save the clicked position as a fish track of length 1 in the
fish basket. That a fish has been counted is indicated by an overlaid graphic circle. Tracking a
marked fish further in consecutive frames is possible by opening the Control dialogs
Manual=>Edit page. See the Edit tracks section below.

Manual tracking method 3: Amp echogram tracking

This method let you track targets by hand drawing in the Amp echogram. It is an extremely
fast manual tracking method but it can only register range and time. Replay in the didson
beam will show the track for all tracked frames and at correct range, but as a circle in the
center beam.
What to do:
a) Check on the Amp echogram tracking check box to enable this tracking option.
b) Press the New track button down
c) Move the mouse to the Amp echogram.
d) In the amp echogram, the cursor will look like a fish when this option is enabled. The
drawing method will be poly free hand line. Press the mouse down and draw a line

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along the trace. End the drawing with a double click.
e) Back in the DIDSON control dialog, Repress the New track button witch now have
the title “Store track”
The method can be combined with the other tracking methods.

Manual tracking method 4: SED tracking

This method can in some situations be more efficient than the other methods ether for
counting or for finding and registering the targets. The method can be carried out without the
DIDSON .ddf files available. Number of targets, time, range, and angle position can be found
together with other features derived from these. Size is found from the echo intensity and not
from the DISON Beam geometry and will probably not reflect the true fish size.

Sonar5-Pro estimate echo angles and create a SED echogram from DIDSON data when the
data is converted. Improved SED echograms can be generated with the Automatic SED
detection method in the DISON control dialog. With a SED echogram available, all the
tracking methods normally associated with ordinary single, dual or split beam systems can be
applied. Using these tools will provide the targets positions in the beam, and the target size.
See the SED Detector section for more about detecting single echoes. See chapter 12 for
more about this tracking option.

Depth by shadows
Shadows can be applied to find a targets vertical position in the water in horizontal
applications. For this to work, it is necessary to tell Sonar 5 about the transducer tilt, and
depth, and to supply the bottom profile under the part of the beam fan where one want to use
the shadows. This is done in the parameter dialog opened by top menu Utilities=>Parameters
=>Application and Hor. profiles.

1. Set up the system for manual tracking

2. Check on the Depth by shadow check box when needed
3. Press New track button down to start tracking
4. Use the mouse in the viewer to mark one echo (picture of a fish in the viewer)
5. Click on the shadow of the fish
6. Repeat from step 2 and 3
7. Press the Store track button or repress the space key to end current track.

The result is reflected in track features dealing with depth, such as the Along ship angle, dist
from surface and dist from bottom.

Editing tracks
Tracks saved in a fish basket can be merged together or deleted. It is also possible to remove
an echo from a track and to add new echoes. One method for editing tracks is described in
chapter 14 about the fish baskets. The other method is to select Track editing in the DIDSON
Viewers menu. This opens the DIDSON control dialog at the Manual=>Edit page.

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Figure 256. Main part of the DIDSON control dialogs Manual => Edit page
When the Edit page is visible, clicking on an existing track seen in the Viewer will select the
track and show its details in the Edit page. To modify the color and line thickness and text,
click the modify button. To delete the currently presented echo in the selected track, press the
Delete echo button. This button indicate witch echo in the track that will be deleted. To add
more echoes, Press the Add more echoes and use the step buttons to go to the frame where
you see the fish echo (picture) that you want to add. See the Manual tracking section for
more about tracking echoes.

Ruler for fish sizing

The ruler page can be used if one only wants to measure fish without tracking them. It is
otherwise used in the same way as the manual tracker. The results are stored as text in the
Ruler’s memo.

Figure 257.DIDSON viewers chart page. The surface and line selector selects whether the
char is to present a smuuthed graph along the line drawn in the echogram or a smothed
chart.

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Upper: Sonar5’s ordinary DIDSON frame view. Lower: Same data presented in the 3D chart.

Intelligent ruler

The intelligent ruler is located in the control dialogs manual page, and it is only visible when
Line or Rectangle is selected as drawing tool. It can be used with the manual ruler, editor and
tracker but for the tracker it will only be available when the “New track” button is down.

When the intelligent ruler is not checked, the system will estimate fish length from the length
of the drawn line or from the diagonal of the drawn rectangle. When checked on, the system
will use the intensity along the drawn line or in the drawn rectangle to find the start and end
of the fish echo. Operator should only ensure to draw the line or rectangle longer, or larger
than the fish echo.

Intelligent ruling with rectangles

Select Rectangle as the drawing tool and check on the “Intelligent ruler”. Set the
running mean filters Range and Beam size (R, B) and select a threshold model in the charts
top panel. Then draw a rectangle that clearly includes the entire fish echo picture. The
algorithm will search for the max and min. intensity within the rectangle and place a threshold
according to the selected threshold model. Echo intensities below the threshold are cut off.
An algorithm will combine the remaining samples into objects and delete all except the
largest. This is done to remove noise and eventual parts of near by fish echoes partly included
in the drawn rectangle. When the most likely fish echo is found, another algorithm will detect

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the "backbone” along the fish echo and calculate the length of this backbone. The rectangle
and the detected backbone are presented in the viewer on top of the fish echo while the chart
will show the part of the echo that was detected and applied in the estimate.

In ruler mode this is done each time you draw a rectangle. In tracking mode the system reacts
only during the actual tracking. If you disagree with the last measured echo during tracking,
you can take that echo out again with one of the buttons in the tracker panel.

When straight line is selected and intelligent ruler is on, then the system compile echo
intensity along the line instead of in the rectangle, but otherwise the principle are the same.
Intelligent ruling with rectangles
This works in the same way as for rectangles, with the only difference that the intensity is
gathered from filtered intensity long the drawn line and not from a rectangle region.

Measuring tail beat frequency

When the converter has been set up to produce max intensity echograms it is sometimes
possible to see larvae feet on the traces in the echogram.
To measure the tail beat frequency, do this:
 Dbl click the Echogram to open the echograms mouse tip monitor.
 Select the menu: “Manual:>Tail beat” in the DIDSON Viewers menu
 Move the mouse into the echogram and click on successive “larvae feet knots in a fish
trace
 End the process by dbl clicking.

By dbl. clicking the mouse, the resulting tail beat frequency will be written to the mouse tip
monitors center page.

Figure 258. Typical fish traces with larvae feet, believed to indicate tail beats.

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Automatic methods

Figure 259. The DIDSON controllers Auto page handles background subtraction, Auto
tracking and single echo detection.
To set up the system for target detection, check on the Show check box in the comparator and
check off the evaluator. Use the setup for the pre-filter and the background to tune the system
to detect targets. Then play the film or go back to the manual tracker to track fish with the
background removed. The fore and background filters can be set up to do classical
background subtraction as well as subtraction by Cross filter target detection.

Automatic tracking
In Figure 259, check on the evaluator and the task, and select the task to be tracking. Then
tune the system so that it tracks the targets well. Observe that the Play button will change
caption to Tracking. Pressing the button start the tracking for the selected part of the
echogram. Press the Select all button and turn on the Multi file checkbox in the control
dialogs left column to track all selected files.

Setup for the tracker

Pressing the setup button in the box named 5-task when the tracker is selected, will open the
tracker setting panel. Here one finds standard tools for a multiple target tracker, adapted to
DIDSON data.
Track support: Set the min. track length to the minimum number of frames for a track. If a
track is observed in less frames than this setting the track will be discarded as noise. In some
cases a target may become invisible for a frame or two. Set the max ping gap to the
maximum number of allowed frames where the track can be missing before the system regard
the track as being cold. A cold track is regarded as passed the beam.

Prediction and gating: When a target pas through the beam and has been observed for the
first time, the predictor tempts to predict where to observe the target in the next frame. The
gating defines the system’s ability to accept deviations from the predicted position. The gating
method will change depending on the selected predictor. Hence one should select the
predictor before one sets the gate.
Predictor = In a box. The operator defines a box around the current observation and the
place this box in the next frame. The observation closest to the center of the box will be the
chosen as next observation of the same target and added to the track.
Prediction = Centerline. A DIDSON target often looks like a thin line piece or an ellipsoid.
A center line can be drawn to both sides. The gating has two parameters. a) The elongation of

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the line, and b) the distance from the line. The line is drawn from the center of the observed
target and (a) samples in each direction. Along this line the system will search for a new
observation in the next frame (b) samples to each side of the center line.
Predict direction checkbox: The predictor has a checkbox for direction. If checked the
system will search for the next observation only in the swimming direction of the target.
Swimming direction can be determined when the second observation of a target has been
found.
Prediction = Degree of overlap: The current fish observation will be used as a template for
where to search in the next frame. The template will be enlarged according to the settings in
the gate. The difference with this selection and the box is that the searched area is not
rectangular but formed as the fish detection in the current frame. Within this fish shaped gate
the system will select the next observation to be the one that overlap most. E.g. the one that
has most pixels in common with the current observation.

Use SED tracker checkbox

If checked the system will tell that it now expect you to use the traditional SED tracker
working on single echo detections in the ordinary SED echogram. These detections are
obtained either during conversion or if you have run the DIDSON dialogs Task 5 with SED
selected.

Singe echo detection

Single echo detections can be used for tracking and classification, and enables many of the
traditional SED based analysis methods. In Figure 259, check on the evaluator and the task,
and select the task to be SED. Then tune the system so that it detects the targets well. Observe
that the Play button will change caption to SED. Pressing the button start the detection for the
selected part of the echogram. Press the Select all button and turn on the Multi file checkbox
in the control dialogs left column to run the SED on all part of all selected files. The system
will generate new SED echograms. Each Detections will be stored with TS, range and athwart
sip angle. Along ship angle will not be available. As for all traditional single echo detections
TS will be the carrier of the fish size. TS is estimated from the detected length by backward
calculation with the selected specie regression. Fish length will later be available by forward
calculation from TS through the same regression.

Producing and exporting track information

From the Viewer
DIDSON Viewer’s upper left menu button has a menu item for export. This will export a
picture of what is seen in the viewer. The Screen grabber found in the Utilities=>Tools menu
can also be used for this.

From the Ruler

The DIDSON ruler opened by Sonar5’s DIDSON Viewer’s upper left menu button store
information about measured targets as text in the Rulers memo. This text can be edited and
copied to clipboard with ctrl+c as and from there pasted to whatever with ctrl+v as with any
other common text editor.

From the Tracker

The DIDSON tracker opened by Sonar5’s DIDSON Viewer’s upper left menu button store

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track information in the fish baskets handled by the Tracker and Classification windows. See
the manual chapter 13 and 14. The baskets have export options that can export the features
selected in the feature library. A track can consist of many single echoes. Each of these
echoes has a set of features that also can be exported from the fish baskets. Single echoes and
track features can also be studied in tools like the Position and Track information window.
See the Analysis=>Data insight menu for these tools.

What information is produced!

Assume that a fish has been observed in five successive frames and that the operator has
pressed down the manual tracking button and tracked the fish in each of these frames before
the track was saved in the fish basket. Then the fish basket will contain one track consisting of
five detections. Each of these detections is stored with information about the line that the
operator did draw in each frame. In addition, each echo will contain a set of point
information telling about the center of the line and the observed target length.
One echo will have the following information
 Backbone: A line running from head to tail of the tracked target in one frame.
 r, ath, alo: Range in meter, along ship and Athwart ship angle in degrees representing
the center of the backbone line in spherical coordinates.
 z, x, y: Cartesian coordinates in meters representing the center of the backbone
line.
 ze, xe, ye: e =exact position. These values are the same as above, but corrected for
transducer platform information like tilt, depth etc given in the Utilities => Parameters
=> Application menu.
 Fish size: Sonar5 convert the length of the backbone into TS with the regression
formula for TS / Length and Length/weight selected in the
Utilities=>System=>Species dialog. The TS is then the key to both length and weight
which both can be selected for output in the feature library.

Note that DIDSON data do not contain vertical target information so the alo. or y values will
be zero unless one have applied Sonar5’s shadow tracking features.

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References
Main menu

Reference to this software:

Balk and Lindem, 2011. Sonar4 and Sonar5 post processing systems, Operator manual
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References SonarX Operator Manual
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