Introduction. Quick Step Procedures. DES Systems Model 241 DES Model 244 DES Model 244 Deep Tow Model 540 Split-Beam Transducers

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1 Introduction The Digitial Echo Processor (DEP) is the software component of HTI's Digital Echo Sounder (DES) System. For a brief description of the DES system refer to the overview section. The Model 241/243/244 DES Systems are full function, state of the art, scientific echo sounders designed for fisheries and other biological research. The are a breakthrough in affordable, scientific-quality hydroacoustic equipment. These systems are designed to address mobile surveys (e.g., in lakes or at sea), and fixed-location applications (e.g., monitoring migrating fish in open rivers or at hydropower dams). HTI Software DEP - (Digital Echo Processor) Interfaces with the Model 241/243/244 DES Systems. DEP provides the interface for properly configuring the DES, adjusting parameters, and visually monitoring the real-time operation of the system during data collection. EchoScape - is a versatile, interactive post-processing program that writes hydroacoustic data to a database, performs data analysis, and displays results. EchoScape offers a straightforward means of selecting individual fish tracks from processed echo based data files output by HTI DES units, Fish traces can be instantly retracked and displayed multiple times. This feature is useful for quickly refining tracking parameters (e.g. minimum target strength, fish direction, etc.) and immediately observing the results. Refer to the EchoScape help file for further information. Help Files This help file is designed to provide information in relation to the DEP (version 05.0 or later) program. Consult the EchoScape and Echoview help files for detailed information on these applications. The primary navigation tool in this help file is the Table of Contents, which includes an Index and Search capability. Additionally, text and image hyperlinks to related information are included throughout. Quick Step Procedures DES Systems Model 241 DES Model 244 DES Model 244 Deep Tow Model 540 Split-Beam Transducers System Installation System Calibration Data Acquisition Acquiring Samples

2 Acquiring Echoes Sampling and Multiplexing Display Reference Main Menus Main Toolbar Main Displays Control Panel System Status Window Echogram Window EchoScope Window 2D Scatter Plot Window 3D Scatter Plot Window Color Bar Window How to Use DEP How to Communicate with DES How to Configure System How to Acquire Data How to Perform Real-Time Fish Tracking How to Post-Process Data File Reference Configuration File Calibraton File Data Files Support Files Appendix Terminology References

3 Overview The Model 241/243/244 DES Systems feature highly accurate time-varied-gains (TVGs), and very stable transmit and receive sensitivities. The systems can be used a short pulse widths, yeilding improved resolution among targets. Standard operation of the systems are via the Windows DEP application. Each DES system includes a Digital Echo Processor and, optionally, incorporates a Digital Multiplex capable of switching or multiplexing among several connected transducers. The transducers can be sampled either sequentially or randomly at pre-determined time intervals. Each system includes simultaneous 20 lotg(r) and 40 log(r) time-varied-gain receiver outputs as standard, and Digital Tape Interface (DTI). With the addition of a Digital Audio Tape (DAT) recorder, the DTI permits recording and playback of the full raw split-beam data. An optional CHIRP FM slide configuration is also available which increases the signal-to-noise ratio for non-reverberant noise by up to 15 db. The DES is durable. In the unlikely event that service is required, contact HTI directly with your DES serial number. All service must be conducted by HTI, or in direct supervision by HTI. Failure to follow this directive will result in voiding of the DES warranty.

4 Hydroacoustic System Components An acoustic transducer converts the echo sounder electrical transmit pulse into an acoustic pulse. In receive mode, it converts the received acoustic signal into a voltage. The transducer beam width is inversely proportional to the size of the transducer and the acoustic frequency, Basic hydroacoustic System

5 Sound Propogation Sound propagation can be pictured as a wave of relative energy of fixed wavelength, and decreasing amplitude moving through an elastic medium. Wave peaks represent areas of compression, C, and troughs represent areas of rarefaction. Diagram of Sound travelling through a medium Frequency Humans hear in the range of approximately 20 Hz to 20 khz. Fish can not hear sound within the range of frequencies commonly used for fisheries research (Figure 2-4), with some rare

6 exceptions Typical frequency range of scientific echo sounders used for fisheries research Typical suitable frequencies for the observation of schools, individual fish, and plankton are shown in the following graph. Range is the approximate maximum distance at which targets might be distinguished from noise.

7 Frequency selection based on Target Type. The advantages of using a high acoustic frequency are the physical size of the transducer will be smaller for a given beam width, and the minimum size object that can be detectged increases with increasing frequency. The disadvantages of a high frequency are the absorption is greater with higher frequencies and there will be greater returns ( echoes) from air bubbles and debris, Acoustic Monitoring of Fish Fish have an internal structure, their air bladder, that effects sound quite easily. This air bladder has a very low density compared to the surrounding medium, water. It is this density difference that causes sound to reflect from the fish, producing an echo. Sound is also reflected off the bones, scales, and flesh of fish. Thus, fish without air bladders

8 (e.g., most catfish and sharks) also produce echoes. However, the amplitude of these echoes is significantly less than echoes from fish of the same size with air bladders Air bladder of cod Gadus mortua compared to those from various other fish (Hawkins 1981). Hydroacoustic monitoring of fish is based on a few relatively simple principles. An acoustic echo sounder transmits a pulse of acoustic energy into the water. The pulse of energy travels through the water at a speed of approximately 1500 m/sec. When the acoustic pulse encounters

9 an object, such as a fish or the bottom, some of the energy (i.e., an echo) is reflected back to the transducer. The echo sounder amplifies the received signal and then sends it to an output device (such as a chart recorder or video display) and/or an echo processor. If the signal level exceeds a mark threshold level, a mark appears on the output display device. The distance from the top of the display to the mark is proportional to the travel time for the pulse to travel from the transducer to the target and back. Since the velocity in water is known, range (distance from the transducer) can be calculated from the travel time. Acoustic Fish monitoring of a fish in a fixed-location site. Pulse Width The acoustic pulse is generated by mechanical vibrations in the transducer. These vibrations introduce a pressure variation in the water which travels away from the transducer at the velocity of sound. The transducer is designed to operate at a particular frequency or vibration rate.

10 The pulse length is one of the factors that affects the spatial resolution of the acoustic system or, for example, the ability to distinguish two fish near each other as individual fish. If more than one fish is within cpl/2, as in the figure below, one will not be able to discriminate them as individual fish. Pulse characteristics of the transmitted acoustic pulse: a) two fish separated in range by R2, and b) illustration of the transmitted acoustic pulse Echoes from fish located at the same range will return to the transducer simultaneously and be indistinguishable. The bottom echo completely masks the presence of fish in the "dead zone," sharply reducing the effective sampling volume. In addition, the echoes from all three fish will overlap with the bottom signal, making them almost impossible to discriminate

11 Discrimination of echo returns from fish targets near the bottom The advantages of using a short pulse length is better range resolution, The disadvantages are the processing of the receiverd echoes from the digital samples may be more difficult for short echoes as well asd the effect of noise on the received echoes is decreased with increased pulse length.

12 Quick Step Procedure 1) Connect Cables Before turning power on to either the DES or the host computer, make sure all cables are connected. The computer must be configured if using a peer to peer (e.g. computer to DES) network connection. 2) Turn on the Echo Sounder First, turn on the DES using the power switch. The DES should respond with asscend beeps. This indicates the DES is properly booted and ready to connect with the host computer. 3) Turn on Computer Next turn on the host computer and wait until Windows has completed its initialization and the desktop display is shown. 4) Start the DEP Application From the Windows screen, double click on the shortcut icon labeled DEP. This starts the acquisition program and will present you with the main window of the application. 5) Open a Configuration The program will use the acquisition parameters or Configuration which was used the last time the program was run. If you wish to use another configuration, select the main toobar button labeled Open Configuration (via a tool tip window) or use the Configuration...Open...main menu option. Select the desired configuration from the dialog's listing. 6. Connect to DES To initiate communication between the DEP Application and the DES, select from the main toolbar select the "Connect to DES" button or from the main menu Commmand->Connect to DES main menu option. After successfully connecting to the DES, the System Status window display will switch from Connected: No to Connected: Yes. 7. Start Processing If you have the correct configuration, select the select from the main toolbar select the "Start Processing" button After successfullly starting the system, the System Status will show the total number of echoes received and the bottom position and tracking mode will appear in the Control Panel. 8. Stop Processing To stop the system, from the main toolbar select "Start Processsing" (it is a toggle between

13 start and stop). This will automatically close the currrent data files. Model 241 Split -Beam Echo Sounder The Model 241 Portable Split-Beam System is a portable version of the Model 244 Digital Splitbeam Echo Sounder multi_frequency_echo_sounder It was designed specifically for hydroacoustic fisheries and plankton evaluations. The Model 241 Echo Sounder provides most of the primary functions of the Model 244 Echo Sounder in a lighter, more compact package that uses less power (runs by 12 VDC). Combining powerful digital signal processing hardware with a Microsoft WindowsXP -based user interface, the Model 241 Echo Sounder can produce results in real-time, with several data display and storage options. With the addition of the Model 540 Split-Beam Transducer(s) and a laptop computer, the Model 241 Echo Sounder is the most advanced, reasonably priced, portable hydroacoustic echo sounder available for fisheries and plankton evaluations. Key Features Samples up to 2 transducers in one frequency (e.g. 120 khz, 200 khz, or 420 khz).

14 High resolution: up to 1400 range strata as small as 10 cm, summary data available as frequently as every 6 sec, and ping rate up to 50 pings/sec. FM slide/chirp signals provide up to a 15 db gain in signal-to-noise ratio, reducing bias and variabillity in resulting fish target strength & biomass estimates. Capable of storing to data files Samples or Processed Echoes. Model 244 Echo Sounder The Model 244 Multi-Frequency System is a dynamic, digital split-beam and single-beam hydroacoustic system. Combining powerful digital signal processing hardware with the DEP application, the Model 244 System produces results in real-time, with multiple data display and storage options. Single Frequency Configuration

15 Key Features Samples up to 16 transducers of up to 5 different frequencies from 38 khz to 1 Mhz. High resolution: up to 1400 range strata as small as 10 cm, summary data available as frequently as every 6 sec, and ping rate up to 50 pings/sec FM slide/chirp signals provide up to a 15 db gain in signal-to-noise ratio, reducing bias and variability in resulting fish target strength and biomass estimates. Multi-Frequency Configuration Model 244 Deep Tow Multi-Frequency System

16 The Model 244 Deep Tow Multi-Frequency System is a powerful, digital split-beam/single-beam hydroacoustic system designed to be towed up to 1000 m (3280 ft) deep. The Model 244 Deep Tow System combines powerful digital signal processing hardware ideal for deep ocean fisheries and plankton research. The menu-driven Windows DEP application permits the operator to enter calibration, operation, and data processing parameters, as well as select realtime data display and output options. Model 244 Echo Sounder and Titanium container. Key Features: Rated to 100 m ( 3280 ft) deep. Samples up to 16 split-beam or single-beam transducers operating at up to 5 different frequencies between 38 khz and 1 MHz. Either slow (timed) or fast multiplex (alternating pings) sampling among all transducers. FM slide/chirp signals provide up to a 15 db gain in signal-to-noise ratio, reducing bias and variability in resulting fish target strength and biomass estimates. MODEL 540 SPLIT-BEAM TRANSDUCERS HTI Model 540 Split-Beam Transducers are available in a variety of frequencies and beam widths. These low noise, preamplified transducers are suitable for applications ranging from mobile surveys in the open ocean, to lakes, to fixed deployments in rivers or at hydropower dams. Both conical-beam and elliptical-beam transducers are available, and all Model 540 Transducers operate with any HTI Model 240-series Split-Beam System.

17 Model 540 Split-beam Transducers Key Features: Each transducer is supplied with detailed calibation information, including transmit and receive sensitivity, beam patterns, and phase angle sitffness plots and parameters. Available split-beam frequencies include 38, 120, 200, and 420 KHZ. Also available are Model 510 Single-Beam Transducers in the same frequencies plus 1 MHZ. Transducer housings made of anodized aluminum standard, bronze optional. Maximum Depth 50 m (16 ft) standard. Flange mount housings available for depths up to 1000 m (3280 ft) Transducer cables Twisted shielded pairs for the transmitter and preamplified transducer signals. Cable lengths m ( ft) standard. Lengths > 305 m (>1000 ft) optional. System Installation Multiplex and Transducer Connections Warning: Use only HTI transducers designed for the frequency of your system (e.g., 200 khz) or the transducer and/or DES may be damaged. A complete hookup diagram for the DES and support components is presented below. Care should be exercised when handling transducers and cables. Dropping a transducer could damage

18 its ceramic element or internal electronics. Do not scratch the epoxy face covering the ceramic element. Before deploying the transducer, gently soap its epoxy face with a solution of one part liquid household detergent to four parts water. The face should be wetted thoroughly and rinsed to eliminate air bubbles. When connecting the transducer cable to the transducer, align the key om tje transducer cable to the connector on the back of the transducer. Improper alignment of the connectors can cause a bent connector pin, or a broken connector. The transducer cables plug into the large 14 pin (Multiplex Outputs) in the back of the DES. The standard Model 241 DES samples one or (optionally) two transducers. The standard Model 243 DES samples one transducer, but can optionally sample up to 16 transducers. The Multiplexing capabilities allow switching between multiple transducers at preprogrammed time intervals, either sequentially or randomly. System Calibration

19 The proper and periodic calibration of hydroacoustic equipment in the laboratory and field cannot be overemphasized as vitally important for quantitative estimation of fish biomass. Calibration can be as simple as using a repeatable gain setting on the chart recorder or as complicated as having the transducer calibrated in an acoustic laboratory. Proper calibration provides the user with information regarding the output power and receiving sensitivity of the complete acoustic system. Calibration assures that an echo produced by a target of known acoustic size, while passing through the axis of the acoustic beam, will produce a known output voltage at the receiver portion of the echo sounder. This information allows the user to determine the effective beam width over which fish of a particular acoustic size will be detected. Since transducers vary in sensitivity, the exact sensitivity must be quantified. By using calibration data, target strength information, and a transducer's beam pattern plot, the effective beam width for the transducer can be determined. Calibration is also required for accurate scaling of integration estimates. Many types of hydroacoustic equipment calibration, such as transducer calibration or overall gain measurements, are beyond the capabilities and resources of most researchers. For these calibrations, the equipment should be periodically returned to the manufacturer or to a qualified acoustic laboratory for such measurements. The actual equipment to be used in the field (including all cables) should be included so that the laboratory calibration will simulate field conditions as closely as possible. Examples of a full system calibration for a split-beam system appears in the Appendix. 1) The Sonar Equation 2) Laboratory Calibrations Beam Pattern Plot Source Level Measurement Transducer/Receiver Sensitivity Measurement Stiffness 3) Standard Target Calibration in the Field The Sonar Equation

20 The sonar equation is the basis for describing the operation of hydroacoustic systems (Figure 4-1). It is used for two purposes. First, it is used during calibration to estimate the source level (SL) and through-system gain (G1) of the hydroacoustic system. Second, the equation is used to calculate receiver gains and chart recorder and analysis thresholds to properly monitor the targets of interest. In the equation below, all factors are expressed in decibels (db). Vo = SL + 2B - 2TL + TS + G1 + Gtvg + RG where Vo = voltage out of the complete hydroacoustic system, at the echo sounder; SL = transducer source level (at a specific transmit level); B = one-way beam pattern factor (0 db for on-axis targets); TL = one-way transmission loss (20 log R + 2aR); TS = target strength (acoustic size); G1 = through system gain, at 1m; Gtvg = time-varied-gain (20 or 40 log R + 2aR); RG = receiver gain level. The echo sounder transmitter emits a pulse of electrical energy which is converted to acoustic energy by the transducer. The measure of the transducer output is SL. The transducer directivity (B(q)), concentrates the pulse of acoustic energy on the axis of the transducer. As the acoustic pulse propagates through the water, its intensity decreases. The transmission loss (TL) is composed of the spreading loss (20 log(r)) and the attenuation (ar). When the pulse hits a target, a portion of the acoustic energy (TS) is reflected back toward the transducer. As the reflected pulse returns, it encounters the same transmission loss (TL). Off axis energy is minimized by B(q). The received acoustic pulse is converted to an electrical signal by the transducer, and amplified by the receiver (G). The detected output (vdet) is measured by processing and display equipment. Note that vdet is only representative of TS when the target is on-axis, and B(q) is 0 db. In the absence of information regarding the position of the target in the beam (B(q)), vdet is only representative of the acoustic signal level present at the face of the transducer. The G term in the equation represents the receiver system gain. G is composed of three terms: Gtvg, RG, and G1. Gtvg is designed to exactly cancel the two-way transmission loss (2TL). RG is the gain which corresponds to the setting of the echo sounder receiver gain control. G1 is the equivalent gain in 1 meter.

21 As noted in the illustration, B(q), SL, and G1 are determined in system calibration. Without these values, it is not possible to make quantitative hydroacoustic measurements. A more detailed description of the calibration of hydroacoustic systems can be found in Albers (1965), MacLennan and Simmonds (1992), and Urick (1975). Beam Pattern Plot To measure a transducer beam pattern, the transducer-under-test (TUT) is mounted on a rotator whose angular position is coupled to a special purpose instrumentation system (Figure 4-2). The echo sounder transmitter is used to generate pulses which are measured by a standard transducer.

22 The two transducers are aligned for maximum on-axis response, and the plotter is normalized for 0 degrees and 0 db. The beam pattern is typically started with the TUT rotated off axis by 90. As the echo sounder transmitter pulses, the TUT is rotated back toward, and then past the standard transducer. The echo level detected at the standard is converted to db and plotted on the beam pattern plotter as a function of the off-axis angle. Source Level With the system transducer TUT and the standard transducer aligned, the system acoustic level (SL) can be measured. The particular standard transducer used will depend on the frequency of the hydroacoustic system. Several models are available for different frequency ranges. Calibration data provided with the transducer relates the Digital Echo Sounder and Digital Echo Processor outputs to the acoustic level at the transducer.

23 System calibrations are not typically performed with transducer separations of 1 meter, thus the voltage reading of the output of the standard must be corrected for one-way transmission loss at the calibration distance Rcal, as detailed in the figure below Sensitivity Measurement Determination of G1 gain requires the on-axis alignment of the system transducer and the standard. The standard is used as the transmitting transducer. Calibration data provided with the standard relates applied RMS volts to the acoustic output level at 1 meter. The known acoustic

24 level is corrected for one-way transmission loss to the system transducer. The measured vdet from the echo sounder, the calculated acoustic level at the system transducer, the computed echo sounder Gtvg, and RG are used to determine the value of G1. Stiffness Several other important measurements are made for split-beam systems. In a manner similar to the measurement of beam patterns, the phase stiffness is plotted relative to angle off axis for split-beam transducers. This is done for both the x and y axis of the transducer, corresponding to the quadrants of the ceramic elements within the transducer. This phase angle to off-axis angle is referred to as the "stiffness" of the transducer. Standard Target Calibration

25 Scientific hydroacoustic systems are usually calibrated prior to delivery, and should be recalibrated periodically. In addition, it is prudent to perform periodic in-situ calibration with a standard target once the system is deployed in the field in the configuration to be used for data collection. Properly implemented, standard target measurements are accurate and simple to perform. The advantage of field (i.e., in-situ) calibration with a standard target is that the echo sounder transmits and receives signals exactly as it would during the acoustic survey. Therefore, the one calibration takes into account the transducer sensitivity, the system gain, and the frequency response of band-pass filters and all other components within the receiver. Field calibration employs a standard target whose acoustic scattering properties are known. The target is normally a homogeneous solid sphere which is suspended below the transducer (Figure 4-5) (or at some distance away, if the transducer is aimed horizontally). The echo sounder is operated in the manner that would be used to collect data, using the same pulse width, timevaried-gain (TVG), transmit power level, and other parameters to be used during the survey. The amplitudes of the echoes produced by the standard target are measured, as well as the range (i.e., distance) to the target. These measurements are sufficient to estimate the combined transmitreceive sensitivity of the transducer. By moving the target across the beam, the position at which the echo is strongest for a given range can be found. This will occur when the target is on the acoustic axis of the transducer. Materials Many types of standard targets have been employed for in-situ standard target calibration, including brass spheres, fishing bobbers, fishing net floats, light bulbs, plastic soda pop bottles (filled with air, or air and lead shot), glass jars (filled with air, or air and lead shot), lead fishing weights, lead down riggers (a.k.a. cannon balls), radar reflectors, toilet bowl floats, oranges, and fish of various sizes (alive, anesthetized, dead, and frozen). Homogeneous spheres make the most reliable standard targets. The acoustic scattering properties of a homogeneous sphere do not change as the target rotates, so the orientation of the sphere is not critical. The amplitude of the echo is determined only by the target's position in the beam. For this and other reasons, use of the non-standard targets listed above (or any target that is not spherical) is not recommended. Nor should any target containing lead be used. Lead tends to absorb acoustic energy and can be easily dented and malformed, resulting in variable acoustic returns. There are three commonly accepted standard targets used for in-situ calibration: table tennis balls, copper spheres, and tungsten carbide spheres. Tungsten carbide and copper spheres have been found to give the best results in practice. The acoustic properties of these targets are discussed by MacLennan and Simmonds (1992). Of the two materials, tungsten carbide standard targets are recommended. Tungsten carbide is more durable, resonates at higher frequencies, and does not corrode (even in sea water).

26 High quality table tennis balls can be used in an emergency (e.g., if you have just dropped your only tungsten carbide target into the water) for frequencies from 200 khz to 420 khz (Welsby and Hudson 1972). A weight must be used below the ball (at least 1 m away) to submerge the table tennis ball (Figure 4-6). Their target strength is typically -41 db to -42 db (depending on the frequency used). Optimum target size must be selected based on the frequency of the echo sounder used (Foote et al. 1983, 1987; MacLennan and Simmonds 1992). The actual target strength of a standard target depends upon the speed of sound in water (which varies primarily with temperature) and system frequency. Table 1 presents the target strengths of tungsten carbide spheres for frequencies from 38 khz to 1 MHz. These targets are best suited to calibrations at the lower frequencies. At very high frequencies, the target strength is less certain because of the close spacing of the resonances. Procedure Do not touch the standard target with your bare hands. Oils from one's fingers may cause air bubbles to adhere to the target. Cotton gloves are recommended. Typically, the standard target is suspended below the transducer, supported by a minimum amount of additional material to avoid unwanted reflections. The attachment medium must be acoustically invisible. This is normally accomplished by encasing the target in a web of monofilament nylon. A fine monofilament mesh bag is frequently used for metal targets. A sixpoint monofilament net bag tied around the sphere is preferable, as it uses a minimum amount of material to secure the target (Figure 4-7). However, care must be exercised with tungsten carbide spheres as they are quite heavy, and can easily break through weak nylon. Take care not to strike the target against rocks. Before it is put into the water, the sphere should be liberally soaked in a detergent solution -- a 5:1 dilution of common household dish washing detergent and fresh water. This wets the surface of the target thoroughly so that air bubbles on the web and standard target are eliminated. Otherwise, air bubbles will effect the acoustic reflectivity of the target. It is generally easier to perform the standard measurements in an area away from currents, wind, debris, and fish. If the calibration is being performed from a vessel anchored in a current or swinging in the wind, the sphere may move unpredictably. A sheltered cove may make a good calibration site. Measurements with horizontally-aimed transducers in fast flowing rivers can be especially challenging. For multi-beam systems (i.e., dual-beam and split-beam), the target does not have to be on-axis. However, it is recommended that the target be located as near to the center as possible, in order to maximize echo amplitude (background noise levels can be relatively high in some environments), and to minimize variability in target strength measurements.

27 The standard target should be a reasonable distance away from the transducer, and certainly beyond the near-field range for the transducer in use. For 200 khz, a minimum range of 3 m is usually sufficient. For most transducers commonly used above 200 khz, a minimum range of 6 m (20 ft) should suffice. Table 4-1. Target strengths of tungsten carbide calibration spheres for sound speeds 1450 m/sec (fresh water) and 1490 m/sec (sea water). Sphere density = 14,900 kg/m3; bandwidth = 5 khz (MacLennan and Simmonds 1992). Frequency Diameter Freshwater TS Sea water TS (khz) (mm) (db) (db) Data Acquistion The DEP program is capable of acquiring two types of hydracoustic data from the DES via the "Command>Acquire..." menus. Selecting these options sets the DES to the selected acquire mode. Sample Data represents the complete unfiltered split-beam acoustic signal as it is output from the DES, before any subsequent application of voltage threshold, echo identification, echo

28 width/shape selection, or other filtering criteria. Sample data is generally used to obtain information on fish biomass. Sample Data Raw Echoes are groups of contiguous digital samples from the Sample Data. The embedded software algorithms in the DES and the DEP program automatically identify, extract and measure each Raw Echo with a peak echo amplitude greater than the minimum detection threshold and write this information written to file. Echo data is generally used to obtain information on individual fish. Raw Echo Data Sample Data The DES digitizes the returning acoustic signal at a 48 khz rate, measuring signal intensity and phase at points spaced approximately every 1/64 of a meter along the waveform (assuming a 1500 m/s speed of sound and two-way sound travel). Each digital measurement or Sample describes the range (Z coordinate), amplitude, and phase (X-Y spatial position) of an evenlyspaced point along the signal. At the point of digitization, the signal has already passed through bandpass and matched filters, but echoes have not been identified or measured. Bandpass filtering removes noise outside of the echosounder frequency band, and the matched filter correlates the returning signal with a time-reversed representation of the transmitted waveform to maximize the output signal-to-noise ratio.

29 Converting Analog Signals to Digital Samples. The Sample (*.SMP) files are stored in binary format at 12 khz. Due to the narrow bandwidth of the acoustic signals, this rate satisfies the minimum Nyquist Theorem sampling rate for this data. The sample files contain the acquisition parameters, calibration settings, and GPS positions (if present). Viewing Sample Data Once Sample data has been collected, the DEP program can be used to view or "playback" a *.SMP file via the Configuration->Open Sample File.. menu option.

30 DEP program playing back a *.SMP data file. Processing Sample Data The DEP program generates only the *.SMP data file within the Acquire Samples mode. To process Sample data files, a post-processing hydroacoustic software package, such as Echoview is required where echo identification and measurement operations are performed.

31 Echoview program displaying an HTI Samples data file. Raw Echo Data The DES performs echo identification and measurement operations on the digitized samples from each ping. Echo processing is based on defined Echo Selection Criteria set within the DEP program.

32 Single Target Echo Pulse Width Measurements Single echoes are isolated by measuring the received echo pulse width at one or more amplitude levels relative to the peak. Measurements can be implemented on digital signal processor (DSP) based processing systems.

33 Diagram showing the Split-beam data Processing with the individual processed echoes being stored in a *.RAW data file. Processing Echo Data The DEP program generates several data file types within the Acquire Echo mode depending on options selected during data collection. There are two main data catagories for processed echoes; Echo Identification Echo Integration

34 Echo Identification Data files with processed Echoes are stored in ASCII based text files. The *.RAW, *.ECH, and *.FSH files contain Echo data and can be viewed and processed further within HTI's EchoScape program. Refer to the EchoScape help files for more information on echo identification processing.

35 EchoScape main screen showing mobile survey data to 40 meters depth and fish traces, with color echogram view and 3-dimensional position data for each echo.

36 EchoScape main screen with zoomed fish traces and selected fish with X-Y plot of selected echoes. Echo Integration During conditions when indvidual echoes cannot be identified ( e.g. high fish desnisities, or schooling fish) a different process must be used to obtain fish biomass information.

37 Single fish echo isolation by pulse length measurement Single echoes can be isolated by measuring the received echo pulse width at one or more amplitude levels relative to the peak. However for multiples echoes the pulse lengths will overlap. Echo Integration provides an unbiased estimate for nonoverlapping and overlapping echoes, Based on the principle that squared signals add incoherently multiple overlapping echoes is the sum of the average values for individual echoes. The Scale factor depends on the average fish backscatttering cross section, pulse length, transducer beam pattern function and constants that are measured during system calibration, Simplified block diagram for echo integration The *.INT files contain Echo Integration data that can be viewed and processed further within HTI's EchoScape program. Refer to the EchoScape help files for more information on echo integration processing.

38 EchoScape main screen showing echo integration data from a mobile survey. Acquiring Samples

39 When the Command>Acquire Samples is selected, the DES acquires the digitial samples for each acoustic signal or "ping" which are displayed in the DEP program. The DEP program acquiring sample data during a mobile survey. Acquire Samples Configuration

40 To Acquire Samples the following settings must be configured within the DEP program. All settings can be stored in a Configuration (*.CFG) file. Sampling Plan Echo Sounder Settings GPS Source Output Data Files Acquiring Echoes When the Command>Acquire Echoes is selected, the Echo Identificaiton process is performed within the DES on the digitial samples for each acoustic signal or "ping".

41 The DEP program acquriing Echo data during a mobile survey. Acquiring Echoes Configuration To Acquire Echoes the following settings must be configured within the DEP program. All settings can be stored in a Configuration (*.cfg) file. Sampling Plan Echo Sounder Settings

42 Echo Criteria Bottom Tracking Real-time Fish Tracking GPS Source Output Data Files Sampling and Multiplexing Data Collection is performed by defining a Sampling procedure or Plan, within the DEP application based on sampling intervals, locations, and various acquisition parameters. A Sampling Plan is comprised of the following components: Sampling Period A Sample Period is a set of data acquistion and transducer calibration settings. In defining the Sample Period's calibration for a particular transducer, a DES Multiplexer Channel must be defined as to where the transducer is actually connected to the back panel of the DES. Although each Sample Period must have a DES Multiplexer Channel specified in order for the system to know what type of transducer is connected (and where), Sample Periods can use the same Multiplex channel number and thus the same transducer within their definitions. Thus, multiplexing between Sample Periods can be accomplished by using just one transducer, or a maximum of 16, the total number of transducers possible that can be connected to the DES. Sample Periods are created or deleted within the Sample Period Summary dialog box.

43 Sequence A Sequence is a specified duration of time in which the DES is instructed to operate. Sequences are created or deleted within the Sequence Summary dialog box. There are several types of Sequence definitions: Idle Sequence: A Sequence which does not contain any Sample Periods. During an idle Sequence the DES will not transmit for that defined duration. An Idle Sequence can be used to avoid cross-talk situations with other echo sounder systems being used or when it is not necessary to sample a particular location within the Sampling Plan. Slow-Mux Sequence: A Sequence which has only one defined Sample Period. The DES will only transmit on the single transducer defined within the Sample Period for the duration of that Sequence. Fast-Mux Sequence: A Sequence which has more than one defined Sample Period. For this type of Sequence the system divides the oveall ping rate defined for that Sequence, across the number of Sample Periods. For example if a Sequence has an overall ping rate of 10 ping per second (pps), with two Sample Periods, the system would alternate the pings between the two, thus in effect each Sample Period would have a ping rate of 5 pps. For a fast multiplexing sequence it is not necessary to have more than one transducer. For the example above, Sample Period one (P1) and Sample Period two (P2) can point to the same transducer. This flexibility allows different parameters to be defined within each Sample Period, such as echo selection criteria, strata definition, fish tracking parameters, or FM slide CHIRP filtering options, all while using the same transducer. A Sequence can have a maximum of 16 Sample Periods defined. However, with multiple Sample Periods there are a number of factors that must be considered such as the Overall Ping Rate for the Sequence and the individual transmit/receive times for each transducer in relation to it's defined range. You must ensure that there is enough time for a transducer to transmit and receive a ping for it's specified range, before switchng to the next transducer or Sample Period. Sampling Plan A Sampling Plan can have any number of Sequences defined in the Sequence Summary dialog box, which are repeated once all have been completed. If the "Sample within Hour" option is enabled, then the total number of Sequences must comprise or "fit" within the hourly interval.

44 Sequence Summary dialog box with an example of "Sample within Hour", with a total of 24 Slow-Multiplexing Sequences. Multiplexing The term Multiplexing refers to switching the DES from one set of data acquisition parameters or Sample Period to another Sample Period within a specificed duration or Sequence.

45 Each DES contains a multiplexor where depending on the model type, up to 16 transducers can be connected to the echo sounder.

46 The Multiplexor Back Panels for a Model 244 DES populated with four channels, and a portable DES's showing the two Multiplexor channels. Slow Multiplexing Each Transducer is sampled within a fixed amount of time or Sequence. This method is generally used at fixed location sites.

47 Plan view of a hydroelectric Dam showing transducer mounts for the spillway and power house sections. Fast Multiplexing Two or more transducers are sampled in the same Sequence where the active transducer is switched after each ping, effectively sampling all transducers simultaneously. Cross section of a river with effective transducers mounted on both shores, fast multiplexing bewteen the all three transducers.

48 For Mobile Surveys the DES system fast-muxes between the "down-looking" and "side-looking" transducers mounted on the same pole. Main Menu The majority of operations available within DEP can be accessed via the main menus. Some operations however, can only be accessed through the program's Main toolbar (i.e. Open and Save Configurations, Connect and Enable DES, data playback, etc.). Configuration View Sampling Plan Setup External Devices

49 Displays Command Help Configuration Menu The options under this menu are for accessing DEP configuration files. A Configuration file is a text based file which contains all parameter settings necessary to operate the DES. Any changes made to the data collection parameters must be saved using the Configuration menus, prior to closing the application. Configuration: Open: Displays a standard "Open" dialog box for selecting an existing Configuration file. Save: Saves any changes made to the current Configuration file. Save As: Displays the "Save As" dialog box for selecting a new file name. Saves all current settings to the newly defined file name Open...Samples File (*.SMP): Displays a standard "Open" dialog box for selecting an existing Samples File for reviewing or "playing back" the samples data. Heading Information: This menu option "toggles" the display for the "Heading Information" dialog box to view the acquistion and calibration settings for the current ping of the current Samples File. Heading Information Dialog box. Close Samples File: This menu option closes the current Samples File, Exit: Ends the DEP program.

50 View Menu Selecting the View... main menu option opens a drop down list of actions applicable to opening and saving the View file (*.vew). The DEP application automatically opens the last View file

51 opened in the program. The View file contains the parameter settings that control the appearance of the various screen display windows (e.g., Echogram, 2D Plot, Echoscope, etc.) and the colorbar definitions. View: Open: Displays a standard "Open" dialog box for selecting an existing View (*.vew) file. Save->: Saves any changes made to the current View file name which is displayed within the menu. Save As: Displays the "Save As" dialog box for selecting a new file name. Saves all current settings to the newly defined file name Toolbar: Check menu option to toggle the display of the main toolbar. Status Bar: Check menu option to toggle the display of hte Status bar. Sampling Plan Menu Selecting the Sampling Plan... main menu option opens a drop down list of parameters applicable to the Sampling Plan. When the application is initially opened, the Sampling Plan parameters are automatically set according to the Configuration file last in use (and saved) when the application was last closed. Sampling Plan: Sequence Summary Displays the Sequence Summary dialog box for configuring the sampling method to be implemented. Sequence Summary Dialog box. Trasnducer Assignment: Displays the "Assign Transducers" dialog box for defining the transducers connected to the DES. Assign Transducers Dialog box.

52 Output Files: Displays the "Output File Options" dialog box to designate the types of files for storing the hydrocacoustic data. Output Files Dialog box Sequence Summary There are two basic Sampling Plan types: Straight Sequence Sampling, and Within Hour Sampling. Straight Sequence Sampling does not key on hourly intervals, but rather uses the duration time of each sequence. When a particular sequence has been completed, the system switches to the next defined sequence in the Sampling Plan and executes that sequence for its duration. When the remaining sequences for the sampling plan have been completed, the system begins again with the first sequence with which it was started when the system was enabled. If there is only one sequence defined for your sampling plan, the system will run the sequence for its duration, then initiate the sequence again. For straight sequence sampling, you must define a Starting sequence. For Within Hour Sampling, the overall sampling scheme keys on hourly intervals. When sampling is initiated, the computer clock is referenced and the defined sequence for that time period is selected. All sample periods start and end times are based on actual clock time, not elapsed time. Since the starting sequence is determined by the computer's clock, you cannot specify a starting sequence for Within Hour Sampling. Note that the Start and End times are in decimal minutes. For example, 5.50 decimal minutes represents 5 minutes, 30 seconds.

53 Switching Sampling Plans To switch to Within Hour Sampling, click on the Sample within Hour check box located in the lower right corner of the dialog box. When selecting this option, a warning message is displayed stating that some existing sequences may be deleted. By switching from Straight Sequence Sampling to Within Hour Sampling, the system will use the duration times of the current sequences for defining the hourly Start and End times of each sequence. If the total straight Sequence times are greater than 60 mins. (the maximum sampling time allowed in Within Hour Sampling), then the Sequences outside of the 60 min. time will be deleted automatically to "fit" the currently defined sequences of one hour's sampling time. By checking the Sample within Hour check box, the Clock Display below the check box will be enabled. The clock display visually displays start and end times for all currently defined sequences for the Within Hour Sampling Plan. To switch from Within Hour Sampling to Straight Sequence Sampling, click on the Sample Within Hour box to uncheck it, thus disabling the option. NOTE: For Sampling Within Hour, the total duration for all sequences must add up to 60 min. If they do not, a warning message will be displayed when you click on the OK button, preventing you from exiting the Sequence Summary dialog box.

54 Parameter Entry -Sequence Summary List Box Description The main list box shows each Sequence as defined for the current sampling plan. A list box or Sequence entry is comprised of the following: 1) Sequence Number: The assigned number for that sequence. A Sequence Number cannot be changed. You can, however, add and delete sequences to change sequence ordering. The symbol "<--" displayed next to one of the defined sequences indicates that this will be the Starting Sequence with which the system will begin when it starts to process data. To change the Starting Sequence, use the mouse to select the desired sequence you wish to start with from the list box. Click on the Change Start Sequence <-- button located to the right side of the dialog box. The list box entry will reflect the new Starting Sequence. NOTE: The "<--" symbol and the Change Start Sequence button are only enabled when the Sampling within an Hour option is NOT checked. 2) Sample Periods: Displays the total number of Sample Periods defined for the Sequence. When a Sequence is initially added (discussed below), it will not have any Sample Periods defined in it, and this entry will display Idle. An Idle sequence is when the DES will not transmit for the specified duration of that Sequence. Adding Sample Periods to a Sequence is accomplished by clicking on the "View" button located above the Sample Period column, or by double clicking on the Sequence list box entry. This displays the Sample Period dialog box which allows you to add and delete Sample Periods from the Sequence. After adding or deleting Sample Periods, the total number will be displayed in the Sample Periods column. 3) Duration: The total time, in minutes, the system will run that sequence. To change the duration of the

55 sequence, use the mouse to select the desired sequence you wish to change. Click inside the Duration Edit Box located directly above the duration column, edit the displayed time and then click on the CHANGE or CHANGE ALL buttons at the bottom of the dialog box. The list box entry will reflect the new duration time. NOTE: When Within Hour Sample is Enabled, Start and End times are automatically calculated for the defined sequences. 4) Start: The beginning time, in decimal minutes, for the sequence within the hour for Within Hour Sampling. NOTE: This field cannot be edited. It is for reference only. 5) End: The ending time, in decimal minutes, for the sequence within the hour for Within Hour Sampling. NOTE: This field cannot be edited. It is for reference only. 6) Ping Rate: The ping rate used for the sequence. If it is a slow-multiplex sequence (only 1 Sample Period), the ping rate is applied just to that sample period. If it is a fast-multiplex sequence (more than one sample period), the ping rate is evenly applied to all sample periods. To change the ending time of the sequence, use the mouse to select the desired sequence you wish to change. Click inside the Ping Rate Edit Box located directly above the ping rate column, edit the displayed ping rate and then click on the CHANGE or CHANGE ALL buttons at the bottom of the dialog box. The list box entry will reflect the new ping rate. 7) Auto Naming (New File and Name) This option is for starting new data files when a sequence is started. With this option off, the data collected from this sequence is saved under the currently named set of data files. With this option on, starting a sequence will cause the current data files to be closed and new data files will be automatically named (see Output Files dialog box) and created. The data from the sequence, and any following sequences, will then be saved under the newly created data files until a sequence with the New Data File option on, is encountered again. A sequence with the New Data File option enabled will cause the current data files to be closed and new data files will be created. To enable the New Data File option, use the mouse to select the desired sequence you wish to change. Click on the "Yes" check box located above the New Data File column and then click on the CHANGE or CHANGE ALL buttons at the bottom of the dialog box. The list box entry will note if the option is enabled by placing a check mark in the column. Parameter Entry -Adding and Deleting Sequences To create or add a Sequence, click on the ADD button located at the bottom of the dialog box. The ADD button is only enabled, however, when the last Sequence of the list box is selected or highlighted. When adding a Sequence, the previous Sequence's parameters are copied into the new Sequence. To delete a Sequence, click on the DELETE button located at the bottom of the dialog box. The DELETE button is only enabled when the last Sequence of the list box is selected or highlighted. Deleting a sequence also removes all defined Sample Periods within that sequence. NOTE: There must always be at least one Sequence, with one defined Sample Period, within a Sampling Plan.

56 Parameter Entry -Changing Sequences The CHANGE and CHANGE ALL buttons are only enabled when editing the Duration, Ping Rate or Auto Naming options. To change a parameter for a particular sequence, first select the sequence from the list box. Select the field you wish to change and type in the new value. Then click on the CHANGE button. The sequence entry in the list box will be updated with the new value. To make a parameter change for all the defined sequences, follow the same procedure described above, except click on the CHANGE ALL button to have the new value assigned to all the sequences Parameter Entry -Randomize Sequences Selecting the Randomize Sequences button displays the dialog box as shown below. This option is for randomizing the Sequence list using a sampling without replacement method. When the current Sequence list is randomized, each Sequence, along with all Sample periods within that Sequence, are positioned in a randomly selected position for the current number of Sequence positions possible. When the dialog is first displayed, the Current Indices and the Randomized section of the list box will be the same. To randomize the Sequences, select the Randomize Ordering button. The Randomized section will show the results of the randomization. The Randomize Ordering button can be selected any number of times. Selecting the OK button of the dialog will assign the Randomized position to the current sequence list. The user may also elect to use the Auto-Randomize function (lower right hand corner of the Sequence Summary Box). If "Hourly" is selected, the sequence order will be randomized at the beginning of each hour. Selecting "Daily" will result in the sequences be re-ordered once per day, at the beginning of the selected hour. Parameter Entry -Sample Period Summary Selecting the "View" button or double clicking on a Sequence list box entry displays the dialog box as shown below. This dialog box is for adding and deleting Sample Periods from the associated Sequence. A maximum of 16 Periods can be defined within a Sequence. Parameter Entry -Sample Period Adding and Deleting To create or add a Sample Period, click on the ADD button located at the bottom of the dialog box. The ADD button is only enabled when there are no Sample Periods defined, or when the last Sample Period of the list box is selected or highlighted. When adding a Sample Period, the previous Sample Period's parameters are copied into the new Sample Period. To delete a Sample Period, click on the DELETE button located at the bottom of the dialog box. The DELETE button is only enabled when the last Sample Period of the list box is selected or highlighted. You may delete all Sample Periods within a Sequence. NOTE: There ust always be at least one sequence, with one defined Sample Period, within a Sampling Plan in order to collect data. Other Sequences in a Sampling Plan however, are not required to have any Sample Periods (i.e. Idle Sequence). Selecting the OK button of the dialog box will save any changes made to the Sample Periods of that Sequence. By selecting the Cancel button, all changes made will be ignored.

57 Assigning Transducers Each transducer, identified by its Calibration file name, is connected to the DES through a Multiplexer port (Mux). Each defined Sequence, with its associated Period, must be associated with the desired transducer. The user should progress through each Sequence and Period, setting the associations according to the desired result. These assignments should be saved using the Configuration...Save or Save As... main menu option. In the sample dialog box shown below, Sequence 3 (S3) has four Periods assigned, each Period is associated with a particular Mux Channel, and each Channel is associated with a Calibration File. To assign Period to Mux associations, click first on the Period radio button, then the Mux Channel button. Clicking on the Calibration Files area on the same level as the Mux Channel will open a dialog box containing the Calibration File parameters. The user should ensure that the correct Cal file has been opened for the particular channel. No Cal file can be associated with more than one Mux Channel. Note, however, that more than one Period may be associated with any one Mux Channel. The number of "Mux Channels/Calibration Files" entries displayed in the dialog box is configuratble by editng the DEP initialization file. Assign Transducer Dialog box configured for a Model 241 DES with 2 channels

58 Assign Transducer Dialog box configured for a Model 244 DES 16 channels

59

60 File Naming There are two data file naming methods: Automatic and Manual file naming. With Automatic File Naming, two options exist. If Hourly Data Files is checked, the system will name files based on the systems current Julian day, hour, and minutes in 24 hour time. In addition it will allow you to designate the starting letter of the files. For example, a RAW file created on April 1 at 12:30 PM with letter "G" designated would be G RAW. The Manual File Naming box can only be edited when the Automatic Naming box is unchecked, therefore to designate a starting letter, first deselect the Automatic Naming option, enter the desired letter, then select Auto Naming. If Verbose Naming is checked, the file will name itself by spelling out the day of week, month, day, and time (Example: Monday April RAW). If the Automatic File Naming option is not on, the Manual File Naming box is enabled. The user may enter any desired name for a file to be created Destinaton for Output Files You may select a preexisting directory when you create and store data files. Use the mouse to click on the Directory Selection button to display the Select Output File Directory dialog box.

61 This is where you change the current data directory. The changes you make will be reflected in the display located directly above the Directory Selection button. Data File Types Acquire Samples Mode There is only one data file type created when acquiring Samples. The Samples (*.SMP) Files are in binary format where each "ping" entry and contains heading information (acquisition parameters, calibration settings, GPS positions ) along with the 12 khz. samples data. Acquire Echoes Mode There are six basic data file types that can be created by selecting the various check boxes. All of the data file types (except the Physical Echo File) are defined on per Sample Period basis using the Sample Period control. The data file types are described below Setup Menu The options under the "Setup..." main menu are for changing parameters for data acquisition and real-time fish tracking. Setup: Echo Sounder: Displays the "Echo Sounder Settings' dialog box. The particular dialog box displayed is dependent on the type of DES specified in the DEP initialization (DEP.ini) file which is configured for the type of Echo Sounder of the system. Echo Sounder Settings Dialog box Echo Selection: Displays the "Echo Selection" dialog box. To select single fish targets within a constant volume of acoustically sampled water, echoes must be selected based on pulse width and position in the acoustic beam. The Echo Selection Criteria dialog box shows the target position (Beam Shape) and pulse width criteria selections available within the DEP. Pulse width criteria (based on the transmitted pulse width) determine which echoes are classified as single targets. Beam shape criteria (along with threshold criteria for the given range) ensure that all single echoes of interest have an equal probability of being selected at a given range. Echo Selection Dialog box

62 Strata Definition: Displays the "Strata Definition" dialog box. This dialog allows the selection of processing strata and permits threshold levels to be set for both single echo processing and echo integration. The Strata Definition dialog box is also where you select echo integration process information for each Sample Period Stata Definition dialog box Bottom Tracking: Displays the "Bottom Tracking" dialog box for selecting how the system detects the bottom location. Bottom Tracking Dialog box Fish Tracking: Displays the "Fish Tracking Settings" dialog box. This dialog enables the realtime fish tracking option as well as configuring the settings for real-time tracking. Fish Tracking Settings Dialog box

63 Transmit Power The Transmit Power control is for setting the level of the transmitter for the current Sample Period. Depending on the type of DES being used, this control has a number of settings. It is recommended that the highest transmit power capable be used for the associated transducer of the Sample Period. WARNING: Do Not use a transmit power level higher than 20 dbw with a 15 transducer! If a knob control is displayed, use the mouse and click on the desired transmit power value shown. If an edit control and a scroll bar are displayed, use the mouse to move the scrollbar until the desired transmit power value is shown in the edit box. Or, type the desired value directly in the edit box. NOTE: For Model 241 systems, within a Fast-Multiplexed Sequence, all Sample Periods must have the same Transmit Power setting. Important: The particular dialog box displayed is dependent on the type of DES specified in the Sounder.ini initialization file The Sounder.ini file is found in the HTI/DEP directory and may be directly edited to associate the appropriate DES. Close the Sounder application prior to editing the ini file. See the file Sounder Ini Log.txt, also in the HTI/DEP directory, for editing information. Pulse Width and Pulse Type Setting the Pulse width is dependent on the selected Pulse type. For the Normal Pulse Type, the pulse width may be selected by moving the displayed scrollbar until the desired Pulse width value is shown in the edit box. A pulse width value can also be entered directly in the pulse width edit box. For CHIRP Pulse Types, the pulse width value is limited to the displayed options. NOTE: When selecting CHIRP pulse types, the pulse width criteria for echo selection <ConfigurationEchoSelectionCriteria.htm> are automatically adjusted for the specified CHIRP pulse type. Factors affecting selection of Pulse Width: The spatial resolution of a system (ability to resolve individual targets) is a function of the pulse length used. Because spatial resolution is increased as the pulse width decreases (inversely proportional), one might expect that the pulse width should be set as short as possible, but this is seldom the case. The ability of an acoustic system to detect noise is a function of the energy in the pulse, which is proportional to the pulse length. Therefore, to optimize the detectability of the echoes in noise, one would like to use a pulse width as long as possible. In practice, the user will generally select the shortest pulse width which will still provide for adequate echo detection. Example <ConfigurationPulseExample.htm> The pulse width selected for riverine applications should probably be as narrow a possible to ensure that fish which move close together in range can be resolved as individual targets. In addition, since the riverine environment is usually noise limited by reverberant noise off of the

64 surface and bottom, if less energy is transmitted into the water (i.e., a shortened pulse width), then this type of noise is reduced. The pulse width entered in the dialog box (see below) is the measurement across the -6 db range of the pulse and is the basis for establishing the Echo <ConfigurationEchoShapeCriteria.htm>Shape Criteria <ConfigurationEchoShapeCriteria.htm>. Systems which utilize <CHIRP.htm> or FM-Slide technology can often achieve pulse widths which are narrower than conventional pulses. The pulse width of normal, or continuous wave pulses are limited by the transducer's ability to begin vibrating and achieve the desired amplitude before the pulse ends. CHIRP or FM slide technology utilizes a long pulse which is then compressed to allow for very narrow output pulses, and corresponding high resolution of targets which are close together in range. Time Varied Gain Time Varied Gain is a successive increase in the amplification of the receiver with range (time) during the during the reception period of each sounding. For single targets, 40 log(r) compensates for geometric spreading loss and absorption. For multiple targets, such as produced by fish schools, a 20 log(r) TVG will provide an output that is a function of the density of the scattering and not a function of range. The Time Varied Gain section is used for setting the TVG for the current Sample Period. It is imperative that the various settings within the TVG section are configured to calculate a correct TVG for the associated transducer for that Sample Period. The different parameters are: Speed of Sound - Enter in meters per second. Speed should be adjusted for temperature and salinity. See Speed of Sound in Water <A-Constant.htm> for calculation method. Type - May be either Normal (gain by db) or Defined (40 log or 20 log - see above). Start/End - Set values to cover the expected range of targets in the study. Minimum distance for the start of the TVG is 2 meters. Crossover - Value to be used may be obtained from the transducer Calibration file. Gain (db) - Sets initial strength of pulse. This gain, in concert with the Receiver gains, are addititive. Blanking Options - May be either Both Start and End, or At End only. Warning: If an incorrect TVG is applied, then fish abundance, as well as the Target Strength, may be incorrectly calculated for all processed echoes. Important: The particular dialog box displayed is dependent on the type of DES specified in the Sounder.ini initialization file The Sounder.ini file is found in the HTI/DEP directory and may be directly edited to associate the appropriate DES. Close the Sounder application prior to editing the ini file. See the file Sounder Ini Log.txt, also in the HTI/DEP directory, for editing information. Tramsitter State The Transmitter State control is used for enabling transmission on a per Sample Period basis. To enable transmission for the current Sample Period, select the ON radio button. To disable transmission, select the OFF radio button. NOTE: In order to actively transmit on a connected transducer, both the Control Panel <Control%20Panel.htm>'s Transmitter switches must be set to ON, and the DES front panel toggle switch must be flipped to the Run position.

65 Important: The particular dialog box displayed is dependent on the type of DES specified in the Sounder.ini initialization file The Sounder.ini file is found in the HTI/DEP directory and may be directly edited to associate the appropriate DES. Close the Sounder application prior to editing the ini file. See the file Sounder Ini Log.txt, also in the HTI/DEP directory, for editing information. Calibrator The Calibrator control is where the calibrator of the DES is turned on and off. To turn on the calibrator, select either the Continuous or Spaced Pulses setting. The Continuous setting will produce a continuous wave from the calibrator. The Spaced Pulses setting will produce pulsed signals spaced apart (in milliseconds) based on the value displayed in the edit box immediately below. To change the spacing, type a new value in the edit box. When the calibrator is on for any Sample Period within the current Sequence, the System Status <Operation-WindowSystemStatus.htm> window will display "CAL" in the current Sequence section. The MX: display will show a "C" for calibrator, rather than the Mux Channel for that Period, to indicate that the data being processed for that Sample Period is from the calibrator of the DES. NOTE: The Transmitter States and the Calibrator States are mutually exclusive. The Calibrator can not be turned on while the Transmitter State is set to either the On or Off setting. Reveiver Gain This control is for determining the receiver gain setting to be used for the current Sample Period. Notice that there are different db steps for the receiver gains depending on the Echo Sounder Model. The knob indicator (red mark) points to the currently selected receiver gain. To change the receiver gain, use the mouse and click on the desired receiver gain value. Adjust receiver gain as appropriate to maximize target detection vs noise levels. Too high a gain may result in saturating the system resulting in a failure to collect usable data.

66 Beam Shape This section is for setting how far off axis an echo, generated by the DES, can be before the DEP will reject it. Typically, the values entered in Minimum and Maximum edit boxes are half the nominal beam width of the associated transducer for that Sample Period. For example, using the circular 15 degree transducer, the Minimum value could be -7.5 and the Maximum value The Nominal beam widths for the transducer are displayed within the Calibration Parameters dialog box. The Minimum Beam Pattern Factor value entered is a global type of criteria applied to echoes with respect to the overall Nominal beam width of the transducer. The Beam Pattern factor is provided by HTI for each transducer it supplies. BPF values typically range from 1.0 E-3 to 8.0 E-3. The BPF can also be found in the Calibration Parameters dialog box, under Transducer Characteristics. Echo Shape Criteria This section is for setting the pulse width shape criteria which each echo, generated by the DES, must meet in order for the DEP to accept it as a valid processed echo. The Pulse Width criteria can be applied to the -6, -12, and -18 db points of the echo"s pulse shape by selecting the appropriate check boxes to the left side of this section. The minimum and maximum values can be entered in either milliseconds or in samples. If values are entered in the milliseconds edit boxes, the associated samples edit box entry will automatically be updated and vice versa.

67 NOTE: Make sure that the Sample Period's pulse width, entered in the Sounder Settings dialog box, will fall between the Minimum and Maximum values (at -6 db) entered in this section. If it does not, then any echoes generated by the DES will not be accepted by the DEP (i.e., displayed or saved to file). Typically, pulse width criteria at -18 db is not used as the pulse width at this level is relatively large and variable. A value of approximately 2-3 samples plus and minus the transmitted pulse width should be sufficient to identify an echo for auto tracking. CHIRP Criteria When CHIRP signals are used the selected bandwidth sets the effective pulse width; transmitter pulse width will have no effect. Using the Bandwidth of 2.5 khz generates a pulse width of 0.72 ms. Thus, the minimum and maximum criteria should be set around this value (e.g. 0.5 ms to 1.0 ms). The 5.0 khz Bandwidth generates a pulse width of 0.36 ms, and the 10.0 khz Bandwidth generates a 0.18 ms pulse width. Minimum and maximum criteria should be set around these values accordingly for the three pulse width measurement points being used. The minimum and maximum values for pulse shape criteria are initially set when changing the pulse type within the Sounder Setting dialog box. These values can then be changed if needed.

68 Strata Editng: Adding or deleting a stratum must always be done at the end of a Sample Period's strata definition table. If the current list box selection is not the last stratum, the Add and Delete buttons are not enabled. The stratum start and end depths will be automatically incremented by the Size(m) value when adding strata. Changing values for a particular stratum is done by editing the values in the edit boxes located above the list box. To change a stratum's parameter, first select the stratum to edit from the list box, then place the cursor within the edit box for the value you wish to edit. Enter the new value, the select the CHANGE button to apply the change. Modify the size of an individual stratum by adjusting the End(m) value; direct modifications of the Size(m) value can only be applied globally with the CHANGE ALL button.by selecting this CHANGE ALL button, when it is enabled, the new value entered will be applied to all strata within that Sample Period. Select ALL from within the Sampling Period selection box to apply the strata values to all sequences and periods. Strata Files: This section is for saving and reading in individual Sample Period's strata definitions that are located in *.CSV (Comma Separated Variables) files. This option allows the user to edit strata definitions outside of the DEP program. To save a strata definition file, click on the Save To (*.csv) File button. A dialog box will be displayed for selecting the location and filename to which you want to save the currently displayed strata definition. To read in a strata definition from a file, select the Open a (*.csv) File button. By selecting the desired file, the contents will be assigned to the currently displayed Sample Period. Selecting the OK button of the dialog box will save any changes made to the strata definitions. By selecting the CANCEL button, all changes will be ignored. Note: As with all parameter changes, the configuration file (on main menu, Configuration...Save / Save As) must be saved prior to closing the application. Failure to save the configuration will result in the parameter changes being lost Fish Density: In some studies, targets are so numerous that it is impractical to either automatically or manually track individual fish. In these instances, fish density (biomass) is estimated based on overall returned signal strength. For each defined stratum, a threshold voltage and a scaler value must be set. Refer to the Echo Integration section for more information. Select echo integration process information for each Sample Period. To do so, check the"enable Integration" check box. The number and/or size of individual strata defined has no effect on the collected data and will not increase the size of the data files. The defined strata are used to

69 associate raw data with a particular stratum and enhance the ability to analyze the data in post processing. NOTE: In order to save integration data to disk, you must have this option checked in the Output Files Options dialog box. Bottom Tracking Mode: Bottom tracking can be done manually using the bottom tracking pot on the DES front panel. The DEP monitor BNC output on the DES front panel indicates where the bottom is being located by the bottom tracking algorithm, the locations of processing strata and locations of all selected echoes. Fixed: The bottom position is located at the value shown in the edit box to the immediate right of the radio control. Setting a fixed depth is useful when the intended study range is less than the depth of the body of water. Manual: The bottom position is set using the Bottom Position Control which is connected to the front panel of the DES. This requires constant attention to accurately follow the bottom contour but is a reliable method to assure accurate results. Echo Scope: A variation of the manual method, the bottom position is set using the Echo Scope

70 display window within the Sounder application. When this tracking mode option is on, the Echo Scope window will show a red circle, or anchor, at the tope of the Current bottom Indicator line. To change the bottom, click and drag this anchor to the desired position. NOTE: In order to use this tracking mode, there must be an Echo Scope display window created. Auto Acquire: Using this tracking option, the bottom position is automatically searched and set, based on the tracking parameters the user has set in the Automatic Bottom Tracking section of the dialog box. When the bottom is lost, the system will first search within the Automatic Bottom window for a peak voltage that is equal to, or greater than the Automatic Bottom Threshold value. If the bottom is not found within the specified number of pings set in the Maximum Missed Pings setting, the system will then being searching for the bottom at the top of the defined strata, progressing down until it finds a peak voltage exceeding the Automatic Bottom Threshold value. NOTE: When the bottom is lost, an audio alarm sounds and a warning display will be shown in the Status Display window. Automatic: This tracking option is similar to the Auto Acquire tracking mode except that when the bottom is lost, it is searched for only within the defined Automatic Bottom Tracking Window. The system will only search within the tracking window until it finds a voltage value that exceeds the Automatic Bottom Threshold value. Channel to Track on: This section is for setting the channel the system will use to automatically track the bottom. Channel 1 is the 40 LogR voltage signal; channel 2 is the 20 LogR voltage signal. Automatic Bottom Tracking: This section is for setting the type of bottom tracking to be used when acquiring and processing data. Window: The Bottom window size, in meters, to use when searching for the bottom in either Auto or AutoAcquire modes, i.e., the auto tracking algorithm will search within the specified distance for another echo which meets the tracking parameter for threshold. Threshold: Value in volts at or above which the echo return may be considered "bottom". Used in either Auto or AutoAcuire modes. Maximum Missed Pings: Used only with the AutoAcquire mode. During a Lost Bottom condition, this is the number of pings the system will use in order to continue searching for the bottom within the tracking window. If a bottom echo is not located by the Max Missed Pings value, AutoAcquire will commence searching for echoes, from the transducer down, that meet the threshold parameter. Fish Tracking Settings In order for the DEP to make correct decisions about which echoes belong to each individual fish, a series of parameters are required which are then incorporated into the target tracking algorithm in the DEP. These criteria allow target tracking in a wide variety of sampling situations, but must be customized to each situation based on water flow, fish behavior, sampling conditions, etc. The Fish Tracking dialog box shows some of the available target tracking

71 parameters. Refer to the How to Perforam Real-time Fish Tracking section. Fish tracking is basically broken up into two parts, tracking criteria and tracking filters. The DEP must first identify a series of processed echoes as a "fish". To do so the DEP uses the parameters entered in the Real-time Criteria section. After the DEP has identified a fish, filtering parameters can be applied to further discriminate the tracked fish. To apply filters, the DEP uses the parameters entered in the Distance in Beam and Average TS section. Real-time Criteria Distance in Beam Average TS This section is where the parameters are entered in order for the DEP to track processed echoes. To change any of the tracking values, select the appropriate edit box and enter in the new value. To enable fish tracking within the DEP, click on the Enable Fish Tracking check box. A check mark will be displayed. To disable Fish Tracking, click on the check box again to remove the check mark. NOTE: In order to save fish tracking data to disk, you must select this option within the Output Files dialog box

72 This section is where the parameters are entered so the DEP can apply the Distance in Beam filter in order to identify tracked fish. To change any of the filter values, select the appropriate edit box and type in the new value. The use should select distance in beam values based on expected or determined effective width of the ensonified beam at the distance where fish echoes are detected. For instance, large distance in beam values would not be appropriate where a significant portion of fish are passing through a narrow section of the beam.

73 This section is where the parameters are entered so the DEP can apply the Average TS filter in order to identify tracked fish. To change any of the filter values, select the appropriate edit box and type in the new value. For fish tracked in dorsal aspect, Love's Formula may be used to determine the approximate target strength expected from a particular length fish. To turn on this filter to Tracked Fish, click on the Turn On check box. External Devices Menu The options under the "Setup..." main menu are for changing parameters for data acquisition and real-time fish tracking. External Devices: GPS/Attidude Source: Displays the "GPS/Attitude Source" dialog box for selecting a GPS unit or Attitude Instrument connected to the computer. GPS/Attitude Source dialog

74 Rotator Positions: With the optional HTI Rotator Controller connected to a serial port of the computer running the DEP, transducers with a connected rotator can have specific positions defined for each designated Sequence in the Sampling Plan. During data colleciton the DEP will automatically send commands to the HTI Rotator Controller to move the rotator(s) to the designated position. The menu option displays the "Rotator Positions" dialog box for designating a Rotator positions. the Rotator Positions dialog box allows for selecting transducer aiming angles for each sequence duration. The dialog box visually shows the pan and tilt positions for the rotator assigned. Rotator Positions dialog COM Port Handler: There are two COM port handlers in the DEP program enabling the program to process data from two sources. For each COM Port Handler you must specify the Serial port and the type of data that will be processed. Serial Port: For the current COM Port Handler, select the Serial port that the Handler will process the data from. Data Type:

75 GPS: If you have a GPS unit, which can output NMEA0183 (v2.00) formatted data (see your GPS unit documentation), first connect the GPS data cable to either COM port 1 or 2 of your computer. Then select the matching GPS port and a Port Handler within the dialog box. Select GPS under Data Type. If the GPS data are formatted correctly, The Latitude, Longitude, and UTC time will be displayed in the System Status window. To disconnect the GPS source within the application, select the None option, freeing up the previously connected COM port. Attitude Indicator: This device attaches to a transducer and provides attitude information (pitch, roll, and magnetic bearing). As with the GPS, Attitude indicator requires that a Port Handler, COM Port, and MUX channel (channel connected to the transducer) be selected. The System allows for simultaneous data collection (via the COM Port Handler) from two devices. By checking the Store all Data to File... check box, all GPS or Attitude information coming into the serial port will be saved into a file called gpsnmea0183.txt. The file is saved in the same directory as the one in which the DEP program is installed. The file is written to continuously until the check box is unchecked. The file and its contents are overwritten whenever the check box is selected again. Supported Identifiers: This button displays the "Supported NMEA0183 type Idenfifiers" dialog box which shows the types of strings the DEP program recognizes. You must verify that the connected GPS unit writes these type of string identifiers to the Serial port of the computer.

76 Main listbox: The main list box displays all Sequences defined in the Sampling Plan. Rotator positions are always applied to the first Sampling Period of a Sequence. Rotators should only be used for a Slow Mux Sampling Plan. ID#: Currently this entry should always match the number in the "Rot:" edit box. This entry is for future support of other rotators. Controller: This section is for designating which Rotator to use for the defined Sequence entries. Cntlr: This entry is always set to 1 (currently only one HTI Rotator Controller can be used with the DEP program). Rot: Enter the Rotator number ( 1 or 2) for the associated Sequence entry. Pan: Enter the Pan position which the Rotator Controller will move the designated Rotator for

77 that Sequence. Tilt: Enter the Tilt position which the Rotator Controller will move the designated Rotator for that Sequence. Delay DES by: Enter the delay, in seconds, to pause the DES processing in order for the rotator to move to the designated location of that Sequence. This ensures data collection is syncrhonized with the rotator positions. CHANGE: Select this button to change the value of the last select edit box, for the selected list box entry. CHANGE ALL: Select this button to change the value of the last select edit box, for all list box entries. DELAYS: Selecting this button will calculate the delays for each sequence based on the rotator number and the positions for each sequence. The calculated values are conservative delay times to ensure the rotator has moved to the desginated position before the DES continues processsing. The delay time for the first Sequence is based on the rotator postions of the last Sequence of the Sampling Plan. Note: The calculated delay times are based on the difference in degrees, between the last and next rotator position with a rotation speed of approximately 0.28 degrees per second. Sample Period Positions: This section depicts visually the defined Pan and Tilt positions along with any designated Offset to be applied for each Rotator position of a Sampling Period. Rotator Controller: This section is for designating which Serial port of the computer a Rotator Control box is connected to along with designating the offsets to use for each Rotator. Number: This control is always set to 1 (only one Rotator Control box can be used with the DEP program). This number is the same as the ID# column of the main list box. Serial Port: Select the serial or COM port of the comptuer that the Rotator Controller is connected to. If the list box selection is set to "NONE", all delay times are set to 0.

78 Offset in Deg: section is for setting the number of degrees which the Pan and Tilt degrees will be offset for each sequence position. Rotator: Each HTI Rotator Controller can control two Rotators. Select the Rotator Number for assigning Pan and Tilt offsets. Pan: Enter the degree offset to be applied to each Pan positon of a Sequence. Tilt: Enter the degree offset to be applied to each Tilt positon of a Sequence. In the example below,the Pan Reference Angle is 45.0 degrees. The Rotator Position display shows the actual degree position. (Sequence Pan Angle + Reference Angle = Actual Rotator Position) to which the rotator will be set. The same is true for the Tilt degree positions. Display Menu The options under the "Display..." main menu are for selecting the types displays for viewing the real-time data. Multiple windows (up to 10) of any type may be created and positioned within the main window. For example a separate set of windows can be created and assigned to each

79 transducer connected to the DES. Display: Echogram: These menu options are for creating and deleting Echogram windows. EchoScope: These menu optiosn are for creating and deleting EchoScope windows. 2D Scatter Plot: These menu optiosn are for creating and deleting 2D Scatter Plot windows. 3D Scatter Plot: These menu optiosn are for creating and deleting 3D Scatter Plot windows. Set All Windows to Auto: This option will enable the "Auto" sequence/period selection in all windows. In "Auto" mode, each plot will be displaying the data currently being collected by the DEP. The current sequence, period, and mux port will be identified in the title bar of the window. Arrange All Windows: Automatically Arranges all windows within the main display by type. Command Menu The options under the "Command..." menu are for communicating and controlling a DES unit which is connected via a network cable. Command: Connect to DES: Check (toggle) menu to establish communication with a connected DES via the required mapped network drive described within the How to Communicate with a DES. After communication has been established, the Sysetm Status Window will be updated. The DEP program uses a proprietary file-based method for communicating with a DES. Unchecking this menu option will disconnect the network connection to the DES unit. Start Processing: Check menu to issue the command to the DES to begin acquiring data. Depending on the Data Acquistion type, various data windows will begin displaying the realtime data.

80 Note: Whenever this option is selected, new data files are created by DEP and all acquired data is automatically stored to file. After unchecking this menu option, you must wait at least one minute before checking the option again in order for the Automatic File Naming feature to correctly create new data files DES Connection: Displays the "DES Connectiont" dialog box for entering the Serial Number of the DES and the Map Network Drive which will be created for communication. The Serial Number of the DES is the "Device Name" DES Connection dialog box Reboot DES: Menu option to reboot the operating system running within the DES via the mapped drive connection. During data acquisition, the DEP program will automatically select this option if it is not receiving data from the DES. In selecting this option a message box will be displayed "You will need to (re)connect the DES, Coninue?" Selecting "Yes" will then reset the DES Acquire Samples: Menu option to configure the DES to Acquire Samples. This option is only enabled when connected to a DES. This menu will be checked if this is the current Data Acquisition mode. Selecting this option does not require reconnecting to the DES. Acquire Echoes: Menu option to configure the DES to Acquire Echoes. This option is only enabled when connected to a DES. This menu will be checked if this is the current Data Acquisition mode. Selecting this option does not require reconnecting to the DES.

81 Serial Number: Enter the Serial Number of the DES unit. This can be found on the front panel of the Echo Sounder. Map Network Drive Enter the desired letter which will be assigned to the DES. Help Menu The options listed under the "Help..." main menu are for accessing the help files of the program, finding out the version of the DEP. Help: Contents: Displays the help file for the DEP program. About DEP: Displays the "About DEP" dialog box.

82 About DEP dialog box. Main Tool Bar The toolbar provides ready access to the most frequently used functions. These and all other functions are available from the drop down menus in the main menu. Open Configuration: Displays a standard "Open" dialog box for selecting an existing Configuration file. Save Configuration: Saves any changes made to the current Configuration file. Connect to DES: Connects/Disconnects communication with the DES, designated in the DES Connection dialog box. Start/Stop Processing: Starts and Stops the real-time data processing from the DES as well as data file storage. About: Display the "About DEP" dialog box. Note: The following tool bar options are only enabled when a Samples File is opened. Start: Sets the position of the Sample file to the start of the file.

83 Forward: Advances the Sample File by one ping. Play: Continously advances the Sample File Pause: Pauses the playing of the Sample File. Main Displays

84 The DEP program showing real-time data for the Acquire Echoes mode. Five types of data displays are possible for output to the main window. Up to ten windows can be created for each type of data display (under the Display main menu option). Thus, a total of 5 x 10 = 50 data display windows can be created, however window management may become overwhelming with any more than five or six total displays at a time. Each display window can be resized by using the mouse and clicking and dragging on the border of the display. The displays can also be minimized or maximized using the buttons located in the upper right corner. You can not close or delete a display window from any of the window's main menus using the buttons located in the upper right corner. Creating and deleting display windows is accomplished under the Display main menu option. A brief description for each type of data display is given below: 1) System Status Shows the overall status of the system. There is only one System Status window within the application. This window should always be visible in order to see the current status of the DEP. 2) Echogram Available for both the Acquire Samples and Echoes mode, this display shows a color representation of the samples comprising each processed echo. The samples are generated by taking the number of samples at the -6 db pulse width, and expanding these values for that particular echo. The current bottom position (red line) is also shown in the echogram display. 3) Echo Scope Available for both the Acquire Samples and Echoes mode, this display shows the maximum amplitude for each processed Sample, or Echo at range, in addition to the current bottom position. 4) 2D Scatter Plot Available only for the Acquire Echoes mode, this display shows the angular echo position in the transducer's beam. Echoes can be viewed in several viewing planes; a) X, Y plane, down the throat of the beam. b) X, Z plane, cross section or horizontal view of the beam. c) Y, Z plane, an overhead view of the beam. 5) 3D Scatter Plot Available only for the Acquire Echoes mode, this display shows the 3-dimensional angular echo position in the transducer's beam. An echo is depicted in the X,Y and Z planes, with its color showing the voltage comprising each processed echo.

85 Control Panel The DES must be connected to the Computer via the Connect to DES command before the options in this panel can be modified.) Trigger: This section is for selecting the trigger source for the DES. In certain situation you may wish to have the sync for the DES com from different sources. Selecting the Int radio button will have the DES sync internally. This is the normal sync source when in the field. If the Ext radio button is selected the DES will expect a sync pulse to be generated externally via

86 the Trigger I/O BNC connection on the front panel of the DES. Selecting the Man radio button will display a button labeled "P" to the right of the option. By clicking on the P button, you can manually sync the DES to one ping and one pint only BNC Sync: This section is for configuring the data output for the Sync Out BNC data connection on the front panel of the DES (i.e., viewing data on an oscilloscope) during data processing. This control is mostly used in fast-multiplexing situations. To output the sync for a specific Sample Period, select the desired Period from the list box selection. To output the sync from all Sample Periods, select the All entry located at the bottom of the list box selections. BNC Output: This section is for configuring the data output for the DES's front panel BNC connection. Located at the top of this section is the list box, which by clicking on the arrow button displays the types of data output. a) Det 40 log --Detected 40 log sum channel output 10 volts peak. b) Det 20 lot --Detected 20 log sum channel output 10 volts peak. c) Sum --Undetected 40 log sum channel at 12 khz. d) Up -- Upper half of beam, undetected 40 log at 12 khz. e) Down --Lower half of beam, undetected 40 log at 12 khz. f) Left --Left half of beam, undetected 40 log at 12 khz. g) Right --Right half of beam, undetected 40 log at 12 khz. Located below the list box are radio buttons representing the front panel BNC connections. For the Model 241 the radio button labeled 1 and 2 represent the BNC connections labeled Det 40 log and Det 20 log respectively. For the Model 243/244 the radio buttons labeled 1, 2, 3, and 4, represent the BNC connection labeled Det 40 lot, Det 20 log, Up, and Left respectively. To view the current data outputs for the BNC connections, click in the desired radio button, and the list box will display the current data type for the connection. To change the current data output of a BNC connection, first select the radio button representing the BNC connection you wish to change. Then select from the list box the desired data type. Note: In selecting a different data type for any of the BNC connections, the User defined Outputs light on the front panel of the DES will be on. This is to designate that the labels for the BNC connections on the front panel may not necessarily match the actual data output, depending on what the user has selected. When the default settings are selected, the User defined Outputs light will turn off. Bottom: This section is for changing the current bottom tracking mode during data processing for the individual Sample Periods within the currently running sequence. Located at the top of this section is a list box for selecting the Sample Period to view or change, and another list box, which, by clicking on the arrow button, displays the types of bottom tracking modes. A description for various tracking modes are as follows: a) Fixed -- Use the defined fixed bottom position. b) Manual -- Use the Bottom Position knob located on the front panel.

87 c) Scope -- Use the control within the Echo Scope Display window. d) Acquire -- Use the Auto-Acquire mode to automatically track the bottom. e) Auto -- Use the Auto-Bottom mode to automatically track the bottom. The various bottom tracking modes are further explained within the Bottom Tracking dialog box. By selecting an entry from the list box, the current bottom tracking mode will be changed instantly. You may also change the data channel to which bottom is applied. To track the the bottom using the 40 lot channel select the radio button labeled 40 log. To track the bottom using the 20 log channel select the radio button labeled 20 Log. When a channel is selected, the current bottom tracking mode will immediately change. During data processing, the current bottom tracking position, no matter what tracking mode is being used, is always displayed within the Bottom at window located at the bottom of the tracking section. System Status Window The section immediately below the title bar is for displaying Run-time Error messages. The figure above shows an example of a Lost Bottom condition. The upper left corner displays whether or not the DEP has been successfully connected to the echo sounder. In addition, it indicates if the system is processing (i.e. data is being sent from the echo sounder to the application), as well as if data is being stored to disk. The associated Hot Key assigned to that particular operation is display to the right. Selecting the F2 function key from the keyboard performs the same operation as selecting the Command Connect to Sounder main menu option. Selecting the F3 function key executes the

88 Command Start Processing toggle menu option. Selecting the F4 function key executes the Command Save Data toggle menu option. The next section below displays the current Sequence that the system is running. The number of Sampling Periods within the current sequence is also displayed, as well as the Multiplex channel on which it is currently being transmitted. The upper right section of the System Status window shows the directory where the data files are being stored, the current available disk space, and total disk capacity of the currently logged disk drive. The section below that shows the current Latitude, Longitude and UTC time which is being sent to the COM port when a GPS source is connected to the computer. If data is being processed via DAT tape, the section will show a Taped display in the lower right corner (as shown). The bottom portion of the Status window shows the real-time statistics for the data being processed when the system is acquiring data being sent from the echo sounder. The current Ping number being processed is shown. The Delta Time display indicates the difference in time between when the data (i.e. binary files) is generated by the DES and when the data (files) is processed by the DEP. The right portion of the real-time statistics section shows the current number of Echoes being processed and their Average TS, along with the current number of Tracked fish and their average TS. The DEP program is capable of acquiring two types of hydracoustic data from the DES via the "Command>Acquire..." menus. The Echogram window is capable of displaying both types of data. Samples Display

89 Figure above shows the Echogram displaying samples data from a mobile survey. Echoes Display

90 Figure above shows the Echogram displaying Echo data from a mobile survey. Echogram Tool bar Auto Scale Selecting the Auto Scale (1st) toolbar button Switches between modes for automatically scaling the Y-axis if the current bottom exceeds the current axis display. If the graph is in auto scale mode, the text above the Y-axis will show Auto. Display Options Selecting the (2nd) toolbar button displays the Echogram Display Options dialog box (Below). Echogram Options Dialog Zoom Out Selecting this (3rd) toolbar button resets the display Previous Zoom Selecting this (4th) toolbar button resets the display to the last selected area

91 The Echogram Display Options dialog box is for setting various options in viewing the Echogram. The Background section is for setting the background color of the echogram. The Color Indicator shows the current background color. Selecting the Edit Color button displays the Color Palette dialog box from which a new color can be chosen. After selecting a color, the Color Indicator will be updated. The Echoes section is for viewing data from individual processed echoes (40 Log) from every ping. The displayed echogram colors are expressed as Volts or Decibels based on the current selection. The Apply Off Axis Criteria option is for applying criteria to the data based on position within the acoustic beam. The position criteria for each individual Sample Period is found in the "Beam Shape" section within the Echo Selection dialog box. If this check box is not checked, then all echoes meeting pulse width and threshold criteria will be shown. The Integration section option is for viewing integration results based on the defined stratum for the current Sample period being displayed. The Echogram shows data at the end of every Sequence switch. The integration display has additional options for displaying integration results in either Volts rms or in absolute Biomass. The calculations for biomass is described in th Appendix. The Maximum Updates/Display edit box is for setting the maximum number of integration reports to be displayed at one time, within the current Echogram window. This can range from 10 to 200. The Echogram's color bar can be hidden by selecting the Hide the Color bar check box. The

92 Origin at Bottom check box option is for setting the origin of the meter (vertical) scale to the lower left corner of the display. This option gives a better perspective of the Echogram display when a transducer is physically located at the bottom of a site looking up. he DEP program is capable of acquiring two types of hydracoustic data from the DES via the "Command>Acquire..." menus. The EchoScope window is capable of displaying both types of data. Samples Display Figure above shows the EchoScope displaying samples data from a mobile survey. The voltage value for the maximum amplitude for each sample is calculated and displayed in blue. Note that there are no strata lines displayed for Sample Data Echoes Display

93 Figure above shows the Echogram displaying Echo data from a mobile survey. The voltage value for each Echo is calculated and displayed in blue. The defined Sample Period's Strata are displayed as grey vertical lines.

94 The 2D Scatter Plot displays the Raw Echoes for the Acquire Echoes mode. Processed echoes are in red and recorded echoes in gray. The red lines represent the nominal beam widths of the transducer associated with the currently displayed Sampling Period. Tool bar Buttons Selecting the ( 1st) toolbar button switches the display for viewing the angular position of the echoes down the throat of the beam. The axes are expressed in degrees of the left/right (x) plane or up/down (y) plane. Selecting the (2nd) toolbar button switches the display for viewing in the left/right versus range plane. The axes are expressed as range in meters (x) and distance from the acoustic axis in meters (y), where negative values are on the right side of the beam. This view provides a plan view of fish passage through the beam when the transducer is aimed horizontally with the "Up" designation on the transducer oriented upward. Selecting the (3rd) button switches the display for viewing in the up/down versus range plane. This view provides a cross-section view when the transducer is aimed horizontally with the "Up" designation on the transducer oriented upward. Selecting the (4th) button displays a dialog for setting the number of recorded echoes (gray in color) to be shown on the screen. By entering 0, only the current echoes (red in color) currently being processed will be displayed. Selecting the unzoom (5th) button, will reset the displays axes to the maximum scale.

95 The 3D Scatter Plot displays the Raw Echoes for the Acquire Echoes mode. The display shows the actual beam dimension for the specified distance from the transducer, depicted as blue cross-hairs, representing the origin of the beam. The origin of the 3D plot is marked with the letters "U" for Up, "D" for down, "L" for left and "R" for right, halves of the transducer. The defined strata is shown as circles or rings along the length of the beam. The cross-hairs at the end of the beam represent the end of the defined strata. Processed echoes are shown by the voltage bin color as in the strata Echogram display. To rotate the 3D plot, move the mouse over the display until the pointer turns into a "Hand" icon. Keeping the left mouse button pressed, move the plot to the desired rotation point, then release the button.

96 Tool bar Buttons Selecting the (1st) toolbar button resets the display to the "Home" position which sets the blue cross-hairs in the middle of the display. Selecting the (2nd) toolbar button displays the 3D Plot Displays Option dialog box. The 3D Plot Display Options dialog box is for setting various options in viewing the 3D plot. The beam's origin can be moved within the window by entering the new origin position in the Origin Position section. You can choose the background of the display, as well as whether you want the beam to have a solid or wire frame, by checking the appropriate option within the Beam Display section. Also within this section is the Hide Beam Interior option. If checked, the interior display of the beam will not be shown, but the processed echoes will still be visible. The echo size can be adjusted by the Echo (point) Size edit section. By default the Visual Distance value will be set to the end of the defined strata for the current Sample Period. By entering in a new value however, the display will limit the beam shape to the desired distance. Selecting the (3rd) toolbar button zooms in on the entire display. Selecting the (4th) toolbar button zooms out the entire display All of the settings shown in the 3D Plot Display Options dialog box, as well as the current rotation of the plot and the currently selected Sample Period Index, are saved within a View (*.VEW ) file when selecting the View Save or View Save As menu options. Color Bar Window This Color Bar window located to the right of the Period window is comprised of 32 Color bar bins. Each color bin can contain a different set of values depending on the option set under the Echogram Display Options. Not all of the Color Bar's bins need to be defined. Undefined bins are displayed white.

97 Color Bar Window - showing Hydrophone colors (left) and voltage colors (right). Color Bins: The settings for each Color Bin can be viewed by clicking on the desired bin which displays the following dialog: Color Bin dialogs showing settings for a hydrophone and a voltage range. Maximum: Edit box for setting the maximum value to represent the Bin Color Minimum: Edit box for setting the minimum value to represent the Bin Color Bin Color: Non-edit box displaying the current Bin Color. Edit Color: Button for displaying the "Color" dialog for selecting a new color.

98 Bin Label: Edit box for setting the label which will be displayed on the Color Bin Color Bar Settings: The Color Bar's settings are updated from two sources: VEW file Contains the voltage bin information when the Color Bar is set to the "volts" display option. The voltage bin values are read in from this text file. Whenever this file type is opened within DEP (as well as when the program is first started) the Color Bar is automatically updated and displays the current settings. The Color Bin dialog allows you to change individual bin settings which will then be reflected in the Color Bar display. However, any changes made will be lost when MarkTags is exited. I How to Communicate with a DES DES Connection Before you can communicate with an DES, there must be a network connection to the actual unit. All DES units are supplied with a network (cross-over) cable which plugs into the front panel of the DES and the computer for a Peer-to-Peer Network connection. Note: In order to communicate with a DES unit the DEP installation program must first be run on the computer. The installation program updates Windows Registry entries necessary for establishing a Network connection. Configuring the Computer The computer to be used with a DES may require configuring it's Network settings. The computer supplied with the system has already been configured to connect directly to the DES. Configuring the Computer

99 Using DEP The standard method of communicating with the DES is through the DEP program, which communicates with the DES unit via a mapped network drive. This communication option requires the following steps: Step 1. Establish Communication Step 2: Disconnecting from the DES Using Remote Desktop Viewing All DES units run Windows CE as its operating system. The Windows CE desktop can be viewed remotely using the "Tight VNC" program. This may be required for configuring advanced settings for the DES system. However, this option is not necessary for normal operation of the DES. Remote Desktop Viewing Viewing DES debug output All DES units have the capability of displaying various runtime statements for debugging purposes. This is an advanced feature and is not required for normal operation. Contact the HTI manufactoring department for more further information on this topic. Viewing DES Debugging Display Computer Network Configuration There are two basic methods for connecting the computer to the DES via a Network connection. I. Peer to Peer Network

100 For this type of network connection where there is no DHCP server, the computer's Network properites must be set to a static Network Address. In addtion a cross-over Network Cable must be used to connect the computer and the DES. Step 1. Displaying Local Area Connection Properties To set the required network properties within Windows 7, go to the Control Panel->Network and Sharing Center. In the "Connections" section "Local Area Connection" and click on the "Properties" button. Windows 7 Local Area Connection Dialog.

101 Step 2. Setting Internet Protocol (TCP/IP) Internet Protocol Version 4 (TCP/IPv4) Properties Dialog box with static IP Address The Figure above shows the settings required to connect directly to a DES unit. It is not necessary to set any "Advanced" settings. After entering the values click on the OK or Close buttons for all dialog boxes. The settings will be retained by Windows whenever the computer is started. Note: A computer configured with above settings will not be able to connect to the internet or a local area (e.g. office) network. When (re) selecting the option "Obtain an IP address automatically", all network settings will be removed requiring you to re-enter the static settings

102 again in order to connect to the DES unit. II. Client Server Network For this type of Network connection requires a Router with DHCP Sever capability which elliminates the need to assign static Network addresses. However, the router will normally need to be configured in order to operate the Client Server Network. Internet Protocol Version 4 (TCP/IPv4) Properties Dialog box configure for non-static IP Address.

103 Step 1. Establish Communication DES Connection Settings In DEP select the DES->Connection menu option to display the DES Connection Settings dialog box. Enter/verify the drive letter mapped to the connected ATDL unit. The designated Serial Number and mapped drive letter is saved within the DEP Initialization file. Connect to DES Select the Command->Connect to DES menu to initialize communication which may take several seconds. After communication is established, the menu option is checked. The System Status window will also be updated showing the "Connected Yes" display. Step 2. Disconnect from the DES To disconnect from the DES, uncheck the Command->Connect to DES option which removes the Mapped Network Drive. The System Status window will also be updated showing the "Connected No" display. Remote Desktop Viewing

104 Connection Details Dialog box. Enter the Serial number (i.e. device name ) of the DES. The default I.P. address of " " can also be entered. DES Console Display.

105 Whenever viewing remotely the WinCE desktop of the DES, the DES console display will be displayed. DES Window CE 5.0 Desktop Display

106 Viewing DES Debugging Display All DES units have the capability of displaying various runtime statements for debugging purposes. To view this debug output a standard serial cable must be connected to the Connector labeled "RS232" located on the Front Panel of the DES. A program must then be used to display the serial output from the DES. The installation files for the "Tera Term Pro" program are included with the DEP software. Run the "Setup.exe' program located in the "\HTI\DEP\Utilities\Tera Term\" folder location. Set the following settings within the Tera Term Pro program: Tera Term New connection Serial Port: Com1 Set this entry to the comport that the serial cable from the DES is connected to. Select the menu option "Setup->Serial Port" Tera Term: Serial port setup: Baud Rate: The display below is an example of a DES debugging statements

107 Tera Term Pro display showing DES ouput. How to Configure System All acquisition parameters are defined by editing the various settings through dialog boxes.

108 These dialog boxes are displayed by selecting the main menu options of the application. Where pertinent, dialog parameters are displayed for each Sample Period defined within the Sampling Plan. To view the current values for a Sample Period, go to the Sample Period Control, which is always located in the upper left corner of the dialog box. Whenever you select a different Sampling Period from this control, the dialog automatically will be updated, displaying the current values for that Sample Period. The Sample Period Control has an ALL option located at the bottom of the list box selections. When the ALL option is selected, any changes made to the displayed values will be applied to all Sample Periods within the Sampling Plan. This allows global changes to be made to selected parameters. All parameters viewed or edited within the DEP can be saved and retrieved via configuration (*.CFG) files, using the options under the Configuration main menu. The DEP supports long file names for saving all parameters within a *.CFG file. Within the Configuration Save As option, it is not necessary to supply the *.CFG file extension since this will be added automatically to the file name. When closing the DEP program, the name of the current configuration file is saved in the Sounder.ini initialization file. When the DEP program is started again, it will attempt to open the configuration file specified in the Sounder.ini file. The name of the currently opened configuration file is shown in the program's title bar located at the very top of the program. Entries in this section describe the various settings necessary for the successful operation of the system and collection of reliable data. These settings, along with the transducer calibration files, constitute the System Configuration and are saved by the user in a file with the format "Name.cfg". Select from the main menu "Configuration...Save" (or "Save As" for a new or alternate configuration). Acquire Samples Configuration Acquire Echoes Configuration How to Acquire Data Note: Ensure that all cables are connected and that the TX Enable/Disable switch is in the Disable position before turning on power to the DES. See Quick Start for a summary of the steps required to activate the system. 1) Connect to DES In the DES Connection dialog box, verify the Serial Number which is found on the front panel of the unit. To initiate communication between the DEP Application and the DES, select from the main

109 toolbar select the "Connect to DES" button or from the main menu Commmand->Connect to DES main menu option. After successfully connecting to the DES, the System Status window display will switch from Connected: No to Connected: Yes. 2) Start Processing Select the Start Processing menu. After successfullly starting the system, the System Status will show the total number of echoes received and the current Bottom Position will show in the Control Panel. Each time the Start Processing option is selected, the current set of echo sounder parameters (e.g., pulse width, ping rate, etc.) for the Sample Period(s) within the starting Sequence, are sent from the DEP to the DES. The DES settings for each Sample Period are listed in the dialog boxes of the Application. After the Start Processing command has been selected, the various displays within the DEP should start updating with data being sent to from the DES, if the proper processing parameters have been set (i.e., Mux Channel connections, Strata thresholds, etc.). A connected oscilloscope should also show the volatage signals coming out of the front panel BNC connections of the DES. 3) Stop Processing Select again (to toggle) the Start Processing menu to stop data processing. The current status of the program can be checked by viewing the System Status Window. The Status Window should always be displayed within the program to monitor the state of data processing. How to Perform Real-time Fish Tracking As each echo is received by the DEP, the angular right angle plane locations for each target echo, as well as its amplitude, range, and target strength, are passed from the DES to the DEP. The DEP software then uses several algorithms to automatically track a target in real-time as it passes through the acoustic beam. The most important tracking parameters are described in the Fish Tracking Settings Dialog. Briefly, a target detection is made up of multiple echoes processed by the DEP. Each target detection will need to fulfill three criteria in order to be classified as a fish. First, it's signal strength must exceed a predetermined threshold, calculated from the minimum target strength (i.e., acoustic size) of interest, as predicted by a size/target strength relationship. According to the pre-data collection calibration of the hydroacoustic system used (see the calibration report provided by HTI for your system), as well as estimates of the minimum size fish of interest, a

110 detection threshold will be set in the echo processor and chart recorder. This target strength threshold is calculated to allow the smallest size class of interest to mark the echogram and be processed by the DEP. This threshold also filters out some of the unwanted noise from various sources of acoustic and electrical interference. Secondly, the target detection must exhibit redundancy. Typically, it must be detected at least four times in succession in order to reliably distinguish it from possible electrical interference or other background interference. Thirdly, a detection must meet user-defined pulse width criteria to correspond to a window around the pulse width used during data collection. During mobile survey data collection, it is recommended that the DES be disabled (using the DES switch), and that DEP data saving be stopped briefly (using the Start/Stop Saving Data tool bar button) at the end of each transect. This places a blank area on the DAT tape, and gives a separate DEP file with a unique name for the data for each transect. This will facilitate postprocessing. If the Automatic file Naming option is selected, the data files (e.g., *.RAW, *.ECH, *.FSH, *.INT, *.SUM files) will be named automatically by the DEP, with the first character in the filename being the letter designated in the Output File dialog box, followed by the Julian date and time the file was created. WARNING: If you open a file, quickly end it, and then open another file within the same minute by restarting processing, you will give the new file the old file's name, appending data to the same file. If the Automatic file Naming option is not selected, then you must manually enter a file name for the data files. All data files will have this name applied along with their assigned file extensions. If a manually named set of data files already exists, the current data will be appended onto these existing files. How to Post Process Data Sample Processing Sample files cannot be accessed directly since these are stored in binary format. A postprocessing program must be used in order to perform Echo Identification and Integration processing. Echo Processing

111 Post processing refers to any additional DEP processing of data which is conducted after realtime data collection. Post-DEP data processing is accomplished by transferring tracked fish files and integration files into spreadsheet or data base software, (e.g., Microsoft Excel, Access). There, data may be sorted by range from the transducer, and weighted spatially and temporally (if sub-sampling has been implemented). Post-processing could include: 1) Weighting the tracked fish detections for the vertical (e.g., in a river) or horizontal (e.g., at a dam) area not sampled by the acoustic beam. For example, this may involve weighting each fish or a sum of fish in a given range strata by the proportion of the water column sampled by the acoustic beam, taking into account any known vertical distribution trends. 2) Extrapolating the weighted counts to times not sampled, usually taking into account any known diel trends in passage rates. 3) Further expanding these weighted, extrapolated counts for additional areas not sampled at all, such as the center of the river (this may require using outside data sources such as test gillnetting). 4) A plethora of distribution computations to characterize the run in time, space and by size (target strength). While these analyses are often easily handled by standard spreadsheets, custom programs may make handling large data volumes more efficient. As most of these analyses are project and site specific, they are typically addressed by the end user. HTI has available ECHOSCAPE, a post processing analysis program specifically designed for use with this application (SOUNDER). ECHOSCAPE is described below: Echoscape is a comprehensive Windows post processing, target tracking, and database conversion program which reads in files created by HTI Models 241, 243, or 244 Split-Beam Systems. These systems all use a single data acquisition program (SOUNDER.EXE) to create *.RAW files (untracked individual echo data), *.ECH files (tracked individual echo data), *.FSH files (tracked fish data), *.BOT files (bottom and location data), and *.INT files (simultaneous echo integration data). RAW files are then combined with any or all of the other types and then converted to a Microsoft ACCESS database file. The database is then displayed on the Echoscape screen as a two dimensional color echogram, a three dimensional display of echoes in the beam, X-Y and X- Z plots, and selected echo data list. Echoscape can then be used to manually enter fish traces in a variety of ways, and/or automatically track echoes. Data can be automatically tracked an unlimited number of times with different tracking parameters than were used during data collection. Manual adjustments may then be made before the data is finally saved as a database. If the original data was echo integrated (an INT file produced), Echoscape can be used to identify and eliminate extraneous data caused by structure or other acoustic noise. To obtain fish bionass estimates the integration must be scaled. Once the data is saved, MS ACCESS may be used to sort, select, summarize and create reports regarding the tracked fish, individual echoes, or echo integration summaries. Within Echoscape, data may be appended at any time by either reading in new RAW, ECH, FSH, BOT, and INT files, or by concatenating previously created databases

112 Configuration File A Configuration file contains all parameter settings necessary to operate the Digital Echo Sounder and Digital Echo Processor system. Changes to the configuration may be made by the user using the other main menu options. Any changes must be saved, using the Configuration menu, prior to closing the application. The user may use the Save As... option to name and save any number of different configurations Configuration files are text (ASCII) files which can be created within MobileTag using the File- >Configuration->Save As" menu option.. Example of a *.CFG file contents [Output File Settings] Enable_Automatic_FileNaming=1 Verbose_Auto_FileNaming=0 Enable_Hourly_Datafiles=1 OutputFile_Name=RECONNECT TEST OutputFile_Directory=C:\HTI_Data\Dep_Data\ Save_Bottom_GPS_Info=0 BottomFile_Interval_InSecs=0 [Reference Angles] Rotator_1=, Rotator_2=, [Mux Channels] Channel_1=Calibrator test 200khz.cal Channel_2=Calibrator test 200khz.cal [ComPort] Handler_1=0,0,0,1 Handler_2=0,0,0,1 [Sampling Definition] Auto_Randomize_Mode=0 Auto_Randomize_Hour=6 SampleWithinAnHour=0 Starting_Sequence=1 Total_Sequences=1 Sequence_1=1,1.00,,,1,0,S

113 [Sequence_1 SamplePeriod_1 Settings] Mux_Channel=1 Transmitter_State=Calibrator_Pulse Transmit_Power=25 Pulse_Width=0.4 Pulse_Spacing=10.0 Period_Interval=100.0 Ping_Rate=100 Receiver_Gain=0 Detected_40Log_Tvg=40.0 Detected_20Log_Tvg=20.0 Tvg_Start=2.0 Tvg_End=100.0 Tvg_Crossover=11.2 Tvg_Gain=0.0 Tvg_Alpha=0.0 Tvg_Blanking=Both Start/End Speed_Sound= Chirp_BandWidth=0.0 Chirp_Pulse_Width=1.25 Use_PW_Criteria_6_12_18=1,0,0 Min_Vert_OffAxis_Angle=-5.0 Max_Vert_OffAxis_Angle=5.0 Min_Horz_OffAxis_Angle=-5.0 Max_Horz_OffAxis_Angle=5.0 Minimum_Beam_Pattern_Factor=-12.0 Min_-6dB_Samples=9 Max_-6dB_Samples=28 Min_-12dB_Samples=5 Max_-12dB_Samples=32 Min_-18dB_Samples=1 Max_-18dB_Samples=36 Enable_Fish_Tracking=1 Ping_Count=5 Ping_Gap=5 Change_Range=0.0 Velocity=4.0 Initial_Slope=0.0 Enable_3D_Tracking=1 Expansion_Exponent=1.0 Distance_Filter_On=0 Distance_PlaneX=0.2 Distance_PlaneY=0.2 Distance_PlaneZ=0.2 Water_Flow_Direction=LeftToRight Average_TS_Filter_On=0

114 Average_Min_TS=-70.0 Average_Max_TS=-10.0 Bottom_Tracking_Mode=Manual Fixed_Bottom_Depth=1.0 Bottom_Window=2.0 Bottom_Threshold=3.0 Bottom_MaxMissed_Pings=5 Rotator_Number=0 Pan_Degree=0.0 Tilt_Degree=0.0 Print_Echogram=0 Print_Integration_Data=0 Print_Start_Range=1.0 Print_End_Range=50.0 Grid_Mark_Spacing=5.0 Printing_Width=8.0 Printing_Threshold=100.0 Paper_Speed=1 Print_Tvg_Channel=40 Save_Raw_Echoes=1 Save_TrackedFish_Echoes=0 Save_TrackedFish=0 Save_Summary_Info=0 Save_Integration_Info=0 [Sequence_1 SamplePeriod_1 Strata] Integration_On=0 Total_Stratum=20 Stratum_1=1.00,6.00,0.100,0.100, e-003 Stratum_2=6.00,11.00,0.100,0.100, e-003 Stratum_3=11.00,16.00,0.100,0.100, e-003 Stratum_4=16.00,21.00,0.100,0.100, e-003 Stratum_5=21.00,26.00,0.100,0.100, e-003 Stratum_6=26.00,31.00,0.100,0.100, e-003 Stratum_7=31.00,36.00,0.100,0.100, e-003 Stratum_8=36.00,41.00,0.100,0.100, e-003 Stratum_9=41.00,46.00,0.100,0.100, e-003 Stratum_10=46.00,51.00,0.100,0.100, e-003 Stratum_11=51.00,56.00,0.100,0.100, e-003 Stratum_12=56.00,61.00,0.100,0.100, e-003 Stratum_13=61.00,66.00,0.100,0.100, e-003 Stratum_14=66.00,71.00,0.100,0.100, e-003 Stratum_15=71.00,76.00,0.100,0.100, e-003 Stratum_16=76.00,81.00,0.100,0.100, e-003 Stratum_17=81.00,86.00,0.100,0.100, e-003 Stratum_18=86.00,91.00,0.100,0.100, e-003

115 Stratum_19=91.00,96.00,0.100,0.100, e-003 Stratum_20=96.00,101.00,0.100,0.100, e-003 Calibration File Each transducer supplied by HTI will be accompanied by a Calibration File (*.cal) which must be designated in the Transducer Assignments dialog box, where each multiplex channel to be used will be matched to an individual transducer. Clicking on the calibration name button will open a Calibration Parameters dialog box, as illustrated below. Click on "Open File" to open a dialog box which will allow you to select the desired transducer to match with the Mux port. Parameters shown, in the "White" windows are those values which were original to the calibration file. Values can be modified using the dialog box, although there should be no reason to directly change the values originally derived. If the file is changed, then it may be saved with a new name by using the "Save File" button Calibration files are text (ASCII) files and can be viewed by any text editor Example of a *.CAL file contents [System Serial Numbers] DES_SN= Transducer_SN= Frequency=120 Maximum_Transmit_Power=2 Average_Watts=12.25 Cable_length=15.2 [Beam Dimension Values] Beam_Shape=Circular Horizontal= Vertical= Beam_Pattern_Factor=4970 [Ratio Values] StiffnessLeftftRightBased=1 Horizontal= Vertical= [Phase Corrections] Horizontal=0 Vertical=0 [Through System Gain]

116 Log_20= Log_40= Tvg_Crossover=11.22 [Coefficent Values] Horizontal_A=0000 Vertical_A=0000 Horizontal_B=0161 Vertical_B=-0048 Horizontal_C= Vertical_C= Horizontal_D=-0264 Vertical_D=0040 Horizontal_E=-0282 Vertical_E=-0308 [Transmit Power Settings] Transmit_Power_1=20.0 Transmit_Power_2=14.0 Transmit_Power_3=8.0 Transmit_Power_4=2.0 Transmit_Power_5=20.0 [Source Level Values] Source_Level_1= Source_Level_2= Source_Level_3= Source_Level_4= Source_Level_5=220 [Comments] Calibration_Date=8/3/10 Comments= Data Files Listed below are the data files created by the DEP program during data acquisition based on the selected Acquire Mode. Acquire Samples: Sample File (*.SMP)

117 Acquire Echoes: Raw Echo File Physical Echo File Fish Echo File Tracked Fish File Summary Fish File Integration File Sample File (*.SMP) This binary data file is created by the DEP program during data acquisition for the Acquire Samples mode. These binary files can only be opened by specific applications capable of opening and parsing the HTI *.SMP file type. Samples files output by HTI Model 241, 243, and 244 Digital Echo Sounder systems contain continuous digital sample data (un-thresholded) from each acoustic transmission or ping. These samples are preceded by a header block of 64, 16-bit data words that describe the echo sounder setup and transducer calibration for the subsequent ping. For HTI Model 24x systems, any echo sounder setting may change on a ping by ping basis, including frequency, pulse width or type, gain, TVG, etc. Ping Header Definitions Ping number = 14 Number of samples in ping = 1600 Next 64 values comprise the Header Block

118 Mux = 0 AES Version = 300 Header = 0, Period = 0 Block = 0 Sequence = 0 Periods per Seq = 4 Header Ver. = 105 DES SW Ver. = 220 AES Delay = 32 DES Model = 243 DES Serial 1 = DES Serial 2 = (shifted 15) DES Serial Num. = XD Serial 1 = 8957 XD Serial 2 = (shifted 15) XD Serial Num. = DES Time - Year = 2008 DES Time - Month = 1, DES Time - Day = 7 DES Time - Hour = 17, DES Time - Min = 50 DES Time - Seconds = Latitude Degrees = N 47 Latitude Minutes 1 = Latitude Minutes 2 = (shifted 15) Latitude Minutes = Longitude Degrees = W 122 Longitude Minutes 1 = Longitude Minutes 2 = (shifted 15) Longitude Minutes = UTC Time - Hour = 1, UTC Time - Min = 47 UTC Time - Seconds = Transducer Frequency = Trigger Source = 1, AES Source = 0 Pulse Period - ms = Cal Pulse Separation - ms = Pulse Width - ms = Transmit Power - dbw = 10 Bandwidth - khz = 0 Filter Type = 0, Filter Num = Log Gain Tap (hex) = 0x8 20 Log Gain Tap (hex) = 0x8 TVG Start Range - meters = TVG Stop Range - meters = TVG Spread 40 Log = 40, blanking = 3 TVG 40 Log Gain - db = 0 TVG alpha - db/km = 0 TVG 20 Log Crossover - meters =

119 TVG 20 Log Gain - db = TVG 20 Log Spread - db = 20 Cal Mode = 1, Cal Type = 1, TX Stat = 0, TX Mode = 0 Source Level - db = Through System Gain - db = Nominal BW Vert. - Degrees = Nominal BW Horz. - Degrees = 10 Electrical Mechanical Angle Ratio V = Polynomial Coefficient U/D b = Polynomial Coefficient U/D c = Polynomial Coefficient U/D d = Polynomial Coefficient U/D e = B-squared 1 = B-squared 2 = (shifted 15) B-squared value = Electrical Mechanical Angle Ratio H = Polynomial Coefficient L/R b = 0065 Polynomial Coefficient L/R c = Polynomial Coefficient L/R d = Polynomial Coefficient L/R e = Through System Gain 20 Log - db = Raw Echo File (*.RAW) This ASCII formatted data file is created by the DEP program during data acquisition for the Acquire Echoes mode. The header information at the top of the file contains settings used during data collection and data column definitions. Rows of data are Raw Echoes that are identified by the digital signal processor (DSP) of the DES. This file contains all echoes that are above the minimum threshold, pass the pulse width criteria, and are within the angle-off axis bounds. Data Column Definitions Ping Number: Ping Number Range Meters: Range (distance) from transducer to echo. Sum Chan. Volts: Amplitude of echo. PW 6dB: pulse width in samples at the -6dB PW 12dB: pulse width in samples at the -12dB PW 18dB: pulse width in samples at the -18dB

120 Up-Dn Angle: Angle off-axis in the "up/down" plane Lf-Rt Angle: Angle off-axis in the "left/right" plane Bottom Meters: Distance from transducer to the detected bottom. Beam P. Factor: Beam Pattern Factor of echo Target Streng: Acoustic size of target in db Sigma value: back-scatterng cross section of the target Mux Port: Channel Port of the DES the transducer is connected Seq Number: Sequence Number of the current Samling Plan Sample Period: Sample Period of the current Sequence Example *.RAT file contents * System: Model 243 Split-Beam Starting Sequence: 1 Date: Wed Nov 18 16:47: (file format version 2.1) * Data processing parameters for Sequence 1 Period FED

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122 Spd _pin Pulse UpToDown * Ping Range Sum Chan. -6dB -12dB -18dB Up-Dn Lf-Rt Bottom Beam P. Target Sigma Mux Seq Sample * Number meters Volts P.W. P.W. P.W. Angle Angle Meters Factor Streng value Port Number Period * Start Sequence = 1 at Wed Nov 18 16:47: Rotator = 0 Pan = 0.0 Tilt = e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e * End of Sequence = 1 at Wed Nov 18 16:47: * Stop Processing at Wed Nov 18 16:56: Physical Echo File (*.BOT) This ASCII formatted data file is created by the DEP program during data acquisition for the

123 Acquire Echoes mode. The header information at the top of the file contains settings used during data collection and data column definitions. Example *.BOT file contents * System: Model 2413 Split-Beam Starting Sequence: 1 Date: Tue Sep 18 20:02: (file format version 1.0) * Data processing parameters for Sequence 1 Period FED

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125 Spd _pin Board_External RightToLeft * Data processing parameters for Sequence 2 Period FED

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127 Spd _pin Board_External RightToLeft * Ping Bottom Latitude Longitude UTC Computer Delta Pitch Roll Compass Mux Seq Sample * Number meters Coordinate Coordinate Time Time Time Degrees Degrees Degrees Port Number Period * Start Sequence = 1 at Tue Sep 18 20:02: Rotator = 0 Pan = 0.0 Tilt = N 0 0 W :00:0 20:02: N 0 0 W :00:0 20:03: N 0 0 W :00:0 20:04: N 0 0 W :00:0 20:05: N 0 0 W :00:0 20:06: N 0 0 W :00:0 20:07: N 0 0 W :00:0 20:08: N 0 0 W :00:0 20:09: N 0 0 W :00:0 20:10: N 0 0 W :00:0 20:11: N 0 0 W :00:0 20:12: N 0 0 W :00:0 20:13: N 0 0 W :00:0 20:14: N 0 0 W :00:0 20:15: N 0 0 W :00:0 20:16: N 0 0 W :00:0 20:17: N 0 0 W :00:0 20:18: N 0 0 W :00:0 20:19: N 0 0 W :00:0 20:20:

128 N 0 0 W :00:0 20:21: N 0 0 W :00:0 20:22: N 0 0 W :00:0 20:23: N 0 0 W :00:0 20:24: N 0 0 W :00:0 20:25: N 0 0 W :00:0 20:26: N 0 0 W :00:0 20:27: N 0 0 W :00:0 20:28: N 0 0 W :00:0 20:29: N 0 0 W :00:0 20:30: N 0 0 W :00:0 20:31: * End of Sequence = 1 at Tue Sep 18 20:31: Ending Ping = * Start Sequence = 2 at Tue Sep 18 20:32: Rotator = 0 Pan = 0.0 Tilt = N 0 0 W :00:0 20:32: N 0 0 W :00:0 20:33: N 0 0 W :00:0 20:34: N 0 0 W :00:0 20:35: N 0 0 W :00:0 20:36: N 0 0 W :00:0 20:37: N 0 0 W :00:0 20:38: N 0 0 W :00:0 20:39: N 0 0 W :00:0 20:40: * Stop Processing at Tue Sep 18 20:40: Ending Ping = 3575 Fish Echo File (*.ECH) This file contains real-time Fish tracking results for the Acquire Echoes mode. This file contains all echoes that have been associated with a Tracked Fish. Example *.ECH file contents * System: Model 2413 Split-Beam Starting Sequence: 1 Date: Fri Sep 21 03:20: (file format version 0.2) * Data processing parameters for Sequence 1 Period FED

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130 Spd _pin Board_External RightToLeft * Data processing parameters for Sequence 2 Period

131 FED

132 Spd-5

133 _pin Board_External RightToLeft * Fish Start End Num. Start Start Range Dist. Dist. Dist. Swim. Target Sigma TS Std. Mx Seq Sample * Num. Ping Ping Ech. Xcoord Ycoord meters X Dir Y Dir Z Dir Speed Streng value Dev. Pt Number Period * Start Sequence = 1 at Fri Sep 21 03:20: Rotator = 0 Pan = 0.0 Tilt = e e e * End of Sequence = 1 at Fri Sep 21 03:30: Ending Ping = 8992 * Stop Processing at Fri Sep 21 04:00: Ending Ping = Tracked Fish File (*.ECH) This file contains real-time Fish tracking results for the Acquire Echoes mode. This file contains summary information for each Tracked Fish. Example *.FSH file contents * System: Model 2413 Split-Beam Starting Sequence: 1 Date: Fri Sep 21 03:20: (file format version 0.2) * Data processing parameters for Sequence 1 Period FED

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135 Spd _pin Board_External RightToLeft * Data processing parameters for Sequence 2 Period FED

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137 Spd _pin Board_External RightToLeft * Fish Start End Num. Start Start Range Dist. Dist. Dist. Swim. Target Sigma TS Std. Mx Seq Sample * Num. Ping Ping Ech. Xcoord Ycoord meters X Dir Y Dir Z Dir Speed Streng value Dev. Pt Number Period * Start Sequence = 1 at Fri Sep 21 03:20: Rotator = 0 Pan = 0.0 Tilt = e e e * End of Sequence = 1 at Fri Sep 21 03:30: Ending Ping = 8992

138 * Stop Processing at Fri Sep 21 04:00: Ending Ping = Summary Tracked Fish File (*.SUM) This file contains real-time Fish tracking results for the Acquire Echoes mode. This file contains summary information for all Tracked Fish. Example *.SUM file contents * System: Model 2413 Split-Beam Starting Sequence: 1 Date: Thu Feb 20 11:21: (file format version 0.1) * Data processing parameters for Sequence 1 Period FED

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145 Spd _pin Board_External RightToLeft * Data processing parameters for Sequence 1 Period FED

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152 Spd _pin Board_External RightToLeft Seq Sample Port Start Stop Sample Raw With Flow Against Flow Num Period Num. Time Time Time Fish Total Weight. Estim. Cumul. Ave.TS Ave.Speed Total Weight. Estim. Cumul. Ave.TS Ave.Speed :21 11:22 0: :22 11:22 0: :22 11:22 0: :22 11:22 0: :22 11:23 0: :23 11:23 0: :23 11:23 0: :23 11:23 0: :23 11:23 0: :23 11:24 0: :24 11:24 0:

153 :24 11:24 0: :24 11:24 0: :24 11:24 0: :24 11:25 0: :25 11:25 0: :25 11:25 0: :25 11:25 0: :25 11:26 0: :26 11:26 0: :26 11:26 0: :26 11:26 0: :26 11:26 0: :26 11:27 0: :27 11:27 0: :27 11:27 0: :27 11:27 0: :27 11:28 0: :28 11:28 0: :28 11:28 0: :28 11:28 0: :28 11:28 0: :28 11:29 0: :29 11:29 0: :29 11:29 0: :29 11:29 0: :29 11:29 0: :29 11:30 0: :30 11:30 0:

154 :30 11:30 0: :30 11:30 0: :30 11:31 0: :31 11:31 0: :31 11:31 0: :31 11:31 0: :31 11:31 0: :31 11:32 0: :32 11:32 0: :32 11:32 0: :32 11:32 0: :32 11:33 0: :33 11:33 0: :33 11:33 0: :33 11:33 0: :33 11:33 0: :33 11:34 0: :34 11:34 0: :34 11:34 0: :34 11:34 0: :34 11:35 0: :35 11:35 0: :35 11:35 0: :35 11:35 0: :35 11:35 0: :35 11:36 0: :36 11:36 0: :36 11:36 0:

155 :36 11:36 0: :36 11:37 0: :37 11:37 0: :37 11:37 0: :37 11:37 0: :37 11:37 0: :37 11:38 0: :38 11:38 0: :38 11:38 0: :38 11:38 0: :38 11:38 0: :38 11:39 0: :39 11:39 0: :39 11:39 0: :39 11:39 0: :39 11:40 0: :40 11:40 0: :40 11:40 0: :40 11:40 0: :40 11:40 0: :40 11:41 0: :41 11:41 0: :41 11:41 0: :41 11:41 0: :41 11:41 0: :41 11:42 0: :42 11:42 0: :42 11:42 0:

156 :42 11:42 0: :42 11:43 0: :43 11:43 0: :43 11:43 0: :43 11:43 0: :43 11:43 0: :43 11:44 0: :44 11:44 0: :44 11:44 0: :44 11:44 0: :44 11:45 0: :45 11:45 0: :45 11:45 0: :45 11:45 0: :45 11:45 0: :45 11:46 0: :46 11:46 0: :46 11:46 0: :46 11:46 0: :46 11:46 0: :46 11:47 0: :47 11:47 0: :47 11:47 0: :47 11:47 0: :47 11:48 0: :48 11:48 0: :48 11:48 0: :48 11:48 0:

157 :48 11:48 0: :48 11:49 0: :49 11:49 0: :49 11:49 0: :49 11:49 0: :49 11:49 0: :49 11:50 0: :50 11:50 0: :50 11:50 0: :50 11:50 0: :50 11:51 0: :51 11:51 0: :51 11:51 0: :51 11:51 0: :51 11:51 0: :51 11:52 0: :52 11:52 0: :52 11:52 0: :52 11:52 0: :52 11:53 0: :53 11:53 0: :53 11:53 0: :53 11:53 0: :53 11:53 0: :53 11:54 0: :54 11:54 0: :54 11:54 0: :54 11:54 0:

158 :54 11:54 0: :54 11:55 0: :55 11:55 0: :55 11:55 0: :55 11:55 0: :55 11:56 0: :56 11:56 0: :56 11:56 0: :56 11:56 0: :56 11:56 0: :56 11:57 0: :57 11:57 0: :57 11:57 0: :57 11:57 0: :57 11:58 0: :58 11:58 0: :58 11:58 0: :58 11:58 0: :58 11:58 0: :58 11:59 0: :59 11:59 0: :59 11:59 0: :59 11:59 0: :59 11:59 0: :59 12: 0 0: : 0 12: 0 0: : 0 12: 0 0: : 0 12: 0 0:

159 : 0 12: 1 0: : 1 12: 1 0: : 1 12: 1 0: : 1 12: 1 0: : 1 12: 1 0: : 1 12: 2 0: : 2 12: 2 0: : 2 12: 2 0: : 2 12: 2 0: : 2 12: 3 0: : 3 12: 3 0: : 3 12: 3 0: : 3 12: 3 0: : 3 12: 3 0: : 3 12: 4 0: : 4 12: 4 0: : 4 12: 4 0: : 4 12: 4 0: : 4 12: 4 0: : 4 12: 5 0: : 5 12: 5 0: : 5 12: 5 0: : 5 12: 5 0: : 5 12: 6 0: : 6 12: 6 0: : 6 12: 6 0: : 6 12: 6 0: : 6 12: 6 0:

160 : 6 12: 7 0: : 7 12: 7 0: : 7 12: 7 0: : 7 12: 7 0: : 7 12: 8 0: : 8 12: 8 0: : 8 12: 8 0: : 8 12: 8 0: : 8 12: 8 0: : 8 12: 9 0: : 9 12: 9 0: : 9 12: 9 0: : 9 12: 9 0: : 9 12: 9 0: : 9 12:10 0: :10 12:10 0: :10 12:10 0: :10 12:10 0: :10 12:11 0: :11 12:11 0: :11 12:11 0: :11 12:11 0: :11 12:11 0: :11 12:12 0: :12 12:12 0: :12 12:12 0: :12 12:12 0: :12 12:13 0:

161 :13 12:13 0: :13 12:13 0: :13 12:13 0: :13 12:13 0: :13 12:14 0: :14 12:14 0: :14 12:14 0: :14 12:14 0: :14 12:14 0: :14 12:15 0: :15 12:15 0: :15 12:15 0: :15 12:15 0: :15 12:16 0: :16 12:16 0: :16 12:16 0: :16 12:16 0: :16 12:16 0: :16 12:17 0: :17 12:17 0: :17 12:17 0: :17 12:17 0: :17 12:18 0: :18 12:18 0: :18 12:18 0: :18 12:18 0: :18 12:18 0: :18 12:19 0:

162 :19 12:19 0: :19 12:19 0: :19 12:19 0: :19 12:19 0: :19 12:20 0: :20 12:20 0: :20 12:20 0: :20 12:20 0: :20 12:21 0: :21 12:21 0: :21 12:21 0: :21 12:21 0: :21 12:21 0: :21 12:22 0: :22 12:22 0: :22 12:22 0: :22 12:22 0: :22 12:22 0: :22 12:23 0: :23 12:23 0: :23 12:23 0: :23 12:23 0: :23 12:24 0: :24 12:24 0: :24 12:24 0: :24 12:24 0: :24 12:24 0: :24 12:25 0:

163 :25 12:25 0: :25 12:25 0: :25 12:25 0: :25 12:25 0: :25 12:26 0: Integration File (*.INT) This ASCII formatted data file is created by the DEP program during data acquisition for the Acquire Echoes mode. The header information at the top of the file contains settings used during data collection and data column definitions. Example *.INT file contents * System: Model 244 Split-Beam Starting Sequence: 1 Date: Fri Feb 22 16:00: (file format version 1.1) * Data processing parameters for Sequence 1 Period FED

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172 Spd _pin Board_External LeftToRight * Start Sequence = 1 at Fri Feb 22 16:00: Rotator = 0 Pan = 0.0 Tilt = 0.0 * Results for Sequence: 1, Sample Period: 1, Mux Port: 1, Total Pings: 52, Aequip: e-002 * Strata Start (m) End (m) Sum Samples Volts (rms) Biomass Sigma * e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e-003

173 e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e-003 * End of Sequence = 1 at Fri Feb 22 16:00: Ending Ping = 51 Support Files Listed below are the file types used by the DEP program to support various display and data acquisition features. Initialization File

174 View File DEP Initialization file Whenever DEP is started and ended the initialization file "DEP.ini" is accessed. This file contains various settings and file names in order for the program to reload the parameters used the last time the program was run. When DEP is first started, the contents of the initialization file are read in, updating all the current program's settings. When DEP is ended, all current settings are written to the initialization file. Some features within DEP can only be set or enabled via the "DEP.ini" file. To set modify these options the file must be edited directly using any text editor (e.g. Notepad, Wordpad, etc). Once the desired option has been set, save the changes to the file and exit the text editor. The options which must be manually set are: [Echo Sounder Model Connected] Model_Number The Model Number must match the type of HTI Echo Sounder. Model,Entry, Descriptions , -----, , 241, old Reciever Gain Taps (-8 db steps), 241, 2413, 243 Receiver Gain Taps (-6 db steps) 243, 243, Basic single frequency 243 system 244, 244, Basic multiple frequency 244, 2443, 244 DES with Linear (243 type) transmitter Mux_Channel The Mux Channel Number must match the number of ports on the back panel of the Echo Sounder. This entry sets the number of "Calibration" buttons are displayed in the Transducer Assignment dialog box. FastMux_System This entry should alway be set to 1.

175 Chirp_System This entry should alway be set to 1. Enable_Acquire_Switch Setting this entry to 0 will disable the Command->Acquire menu options prevening the capability of changing the Acquire mode of the DES. Setting this entry enables the Acqire menus, [Internal Settings] Acquire on Startup This enables the option to have the DEP program Start Processing and start data collection whenever the program is started. This feature is normally used at remote site locations. In order to use this feature, The DEP program must be configured to start when the Windows operating system is started (i.e. Startup folder). Enable_GPStoDES This entry should alway be set to 1 to have the current GPS information (via the DEP program) sent to the DES to store this information in the heading section of each Ping for a Samples file. Bottom_Position_Knob_Scaler This entry is for setting the sensitivity of the Bottom Position knob on the front panel of the DES. The smaller the number the LESS sensitive ( more turning is required) in changing the bottom location. Max_Raw_Echo_Voltage This value is sent down to the DES in setting a global threshold in volts. Any processed echoes. above this threshold will be removed. Reboot_DelaySecs The amount of time the DEP waits for a response from the DES when actively procssing. If the DES is not responding after the specified amount of time, the DEP will attempt to reboot the DES and restart procsssing. [Demo_Files] This section is for configuring the DEP program to run in a demonstration mode and is not

176 required for normal data processing. All other entries within the Initialization file are automatically updated when DEP is ended. Listed below is an example of an "DEP.ini" file. Entries which must be manually set as described above are highlighted. Example DEP.INI file contents [Echo Sounder Model Connected] Serial_Number=DES Network_Drive=S: Model_Number=2413 Mux_Channels=2 FastMux_System=1 Chirp_System=1 Enable_Acquire_Switch=0 [Internal Settings] Acquire_On_Startup=0 Enable_GPStoDES=1 Bottom_Position_Knob_Scaler=32767 Max_Raw_Echo_Voltage=1 Internal_Trigger=1 Reboot_DelaySecs=120 Last_Configuration=C:\HTI\DEP_0500\Example_Files\calibrator test 200kHz.cfg Last_View=C:\HTI\DEP_0500\Example_Files\calibrator test.vew [Demo_Files] Demo_Enabled=0 Demo_Model_Type=2413 Demo_Binary_Folder=S:\HTI\Binary Demo_Start_Number=1 Demo_End_Number=82 Demo_Sample_Fields=4 MoveTo_BinaryFile_Folder= [Main Window size] Rect= icon=0 max=1 tool=1 status=1

177 View (*.vew) Files View files are mostly used to customize the main display ( e.g. Data Windows and color bar schemes) of the DEP program. View files are text (ASCII) type files which can initially be created within DEP using the View...Save As menu option. Below is an example of a typical view file. View File Example: [Display Windows] 3D_Plot=1 Echo_Scope=1 Echogram=1 2D_Plot=1 Density=0 Fish_By_Range=0 Fish_By_Angle=0 [Voltage Color Bins] Bin_1=0000,7943,0,0,96,0.01 Bin_2=7943, ,0,0,128,0.01 Bin_3= , ,0,0,160,0.01 Bin_4= , ,0,0,192,0.02 Bin_5= , ,0,0,223,0.02 Bin_6= , ,0,96,255,0.03 Bin_7= , ,0,128,255,0.03 Bin_8= , ,0,160,255,0.04 Bin_9= , ,0,192,255,0.05 Bin_10= , ,0,223,255,0.06 Bin_11= , ,0,255,224,0.08 Bin_12= , ,0,255,192,0.10 Bin_13= , ,0,255,160,0.13 Bin_14= , ,0,255,128,0.16 Bin_15= , ,0,255,96,0.20 Bin_16= , ,96,255,0,0.25 Bin_17= , ,128,255,0,0.32 Bin_18= , ,160,255,0,0.40 Bin_19= , ,192,255,0,0.50 Bin_20= , ,223,255,0,0.63 Bin_21= , ,255,224,0,0.79 Bin_22= , ,255,192,0,1.00 Bin_23= , ,255,160,0,1.26 Bin_24= , ,255,128,0,1.58 Bin_25= , ,255,96,0,2.00 Bin_26= , ,255,0,0,2.51 Bin_27= , ,160,160,160,3.16

178 Bin_28= , ,128,128,128,3.98 Bin_29= , ,96,96,96,5.01 Bin_30= , ,64,64,64,6.31 Bin_31= , ,32,32,32,7.94 Bin_32= ,10000,0,0,0,1 [Decibel Color Bins] Bin_1=-10,-98.00,0,0,255, Bin_2=-98.00,-96.00,0,32,255, Bin_3=-96.00,-94.00,0,64,255, Bin_4=-94.00,-92.00,0,96,255, Bin_5=-92.00,-9,0,128,255,-9 Bin_6=-9,-88.00,0,159,255, Bin_7=-88.00,-86.00,0,191,255, Bin_8=-86.00,-84.00,0,223,255, Bin_9=-84.00,-82.00,0,255,255, Bin_10=-82.00,-8,0,255,223,-8 Bin_11=-8,-78.00,0,255,191, Bin_12=-78.00,-76.00,0,255,159, Bin_13=-76.00,-74.00,0,255,128, Bin_14=-74.00,-72.00,0,255,96, Bin_15=-72.00,-7,0,255,64,-7 Bin_16=-7,-68.00,0,255,32, Bin_17=-68.00,-66.00,0,255,0, Bin_18=-66.00,-64.00,32,255,0, Bin_19=-64.00,-62.00,64,255,0, Bin_20=-62.00,-6,96,255,0,-6 Bin_21=-6,-58.00,128,255,0, Bin_22=-58.00,-56.00,159,255,0, Bin_23=-56.00,-54.00,191,255,0, Bin_24=-54.00,-52.00,223,255,0, Bin_25=-52.00,-5,255,255,0,-5 Bin_26=-5,-48.00,255,223,0, Bin_27=-48.00,-46.00,255,191,0, Bin_28=-46.00,-44.00,255,159,0, Bin_29=-44.00,-42.00,255,128,0, Bin_30=-42.00,-4,255,96,0,-4 Bin_31=-4,-38.00,255,64,0, Bin_32=-38.00,-36.00,255,32,0, [Voltsrms Color Bins] Bin_1= e-010, e-010,0,0,96,1.6e-010 Bin_2= e-010, e-010,0,0,128,2.5e-010 Bin_3= e-010, e-010,0,0,160,4.0e-010 Bin_4= e-010, e-010,0,0,192,6.3e-010 Bin_5= e-010, e-009,0,0,223,1.0e-009 Bin_6= e-009, e-009,0,96,255,1.6e-009 Bin_7= e-009, e-009,0,128,255,2.5e-009 Bin_8= e-009, e-009,0,160,255,4.0e-009 Bin_9= e-009, e-009,0,192,255,6.3e-009 Bin_10= e-009, e-008,0,223,255,1.0e-008 Bin_11= e-008, e-008,0,255,224,1.6e-008 Bin_12= e-008, e-008,0,255,192,2.5e-008 Bin_13= e-008, e-008,0,255,160,4.0e-008 Bin_14= e-008, e-008,0,255,128,6.3e-008

179 Bin_15= e-008, e-007,0,255,96,1.0e-007 Bin_16= e-007, e-007,96,255,0,1.6e-007 Bin_17= e-007, e-007,128,255,0,2.5e-007 Bin_18= e-007, e-007,160,255,0,4.0e-007 Bin_19= e-007, e-007,192,255,0,6.3e-007 Bin_20= e-007, e-006,223,255,0,1.0e-006 Bin_21= e-006, e-006,255,224,0,1.6e-006 Bin_22= e-006, e-006,255,192,0,2.5e-006 Bin_23= e-006, e-006,255,160,0,4.0e-006 Bin_24= e-006, e-006,255,128,0,6.3e-006 Bin_25= e-006, e-005,255,96,0,1.0e-005 Bin_26= e-005, e-005,255,0,0,1.6e-005 Bin_27= e-005, e-005,160,160,160,2.5e-005 Bin_28= e-005, e-005,128,128,128,4.0e-005 Bin_29= e-005, e-005,96,96,96,6.3e-005 Bin_30= e-005, e-004,64,64,64,1.0e-004 Bin_31= e-004, e-004,32,32,32,1.6e-004 Bin_32= e-004, e-004,0,0,0,2.5e-004 [Biomass Color Bins] Bin_1= e-010, e-010,0,0,96,1.6e-010 Bin_2= e-010, e-010,0,0,128,2.5e-010 Bin_3= e-010, e-010,0,0,160,4.0e-010 Bin_4= e-010, e-010,0,0,192,6.3e-010 Bin_5= e-010, e-009,0,0,223,1.0e-009 Bin_6= e-009, e-009,0,96,255,1.6e-009 Bin_7= e-009, e-009,0,128,255,2.5e-009 Bin_8= e-009, e-009,0,160,255,4.0e-009 Bin_9= e-009, e-009,0,192,255,6.3e-009 Bin_10= e-009, e-008,0,223,255,1.0e-008 Bin_11= e-008, e-008,0,255,224,1.6e-008 Bin_12= e-008, e-008,0,255,192,2.5e-008 Bin_13= e-008, e-008,0,255,160,4.0e-008 Bin_14= e-008, e-008,0,255,128,6.3e-008 Bin_15= e-008, e-007,0,255,96,1.0e-007 Bin_16= e-007, e-007,96,255,0,1.6e-007 Bin_17= e-007, e-007,128,255,0,2.5e-007 Bin_18= e-007, e-007,160,255,0,4.0e-007 Bin_19= e-007, e-007,192,255,0,6.3e-007 Bin_20= e-007, e-006,223,255,0,1.0e-006 Bin_21= e-006, e-006,255,224,0,1.6e-006 Bin_22= e-006, e-006,255,192,0,2.5e-006 Bin_23= e-006, e-006,255,160,0,4.0e-006 Bin_24= e-006, e-006,255,128,0,6.3e-006 Bin_25= e-006, e-005,255,96,0,1.0e-005 Bin_26= e-005, e-005,255,0,0,1.6e-005 Bin_27= e-005, e-005,160,160,160,2.5e-005 Bin_28= e-005, e-005,128,128,128,4.0e-005 Bin_29= e-005, e-005,96,96,96,6.3e-005 Bin_30= e-005, e-004,64,64,64,1.0e-004 Bin_31= e-004, e-004,32,32,32,1.6e-004 Bin_32= e-004, e-004,0,0,0,2.5e-004 [Status Window size] Rect=

180 icon=0 max=0 hide=0 [3D_Plot_1 Window] Rect= icon=0 max=0 hide=0 Sequence=0 Period=0 Auto_Switch_Mode=0 Display_Type=0 RotationX=33 RotationY= ScaleX= ScaleY= ScaleZ= Visual_Distance=51.00 OriginX=0000 OriginY=0000 Echo_Point_Size=4.0 Hide_Interior=0 Wired_Frame=0 White_Background=0 [Echo_Scope_1 Window] Rect= icon=0 max=0 hide=0 Sequence=0 Period=0 Auto_Switch_Mode=0 [Echogram_1 Window] Rect= icon=0 max=0 hide=0 Sequence=0 Period=0 Auto_Switch_Mode=0 Display_Type=0 Max_Distance=10 Max_Reports=200 Hide_Colorbar=0 Background_Color=255,255,255 Apply_OffAxis_Criteria=1 Bottom_Origin=0 [2D_Plot_1 Window] Rect= icon=0 max=0

181 hide=0 Sequence=0 Period=0 Auto_Switch_Mode=0 Graph_Type=0 External Devices Appendix CHIRP Signal Described Target Strength versus Fish Length Estimation Scaling Integration Data Calibration Sheets CHIRP Signals CHIRP Signals (FM-Slide) CHIRP (FM Slide) was developed as a means of putting more transmit power into the water, while keeping the effective pulse width relatively short. The result is an increase in the signalto-noise ratio, while retaining the range resolution inherent in the short pulse width. Briefly, the generated pulse is a wide band signal which incorporates a sliding change in frequency over the length of the pulse (Frequency Modulated-Slide). The receiver, using an electronic filter, detects the echo by means of its frequency "signature" and compresses the signal to emulate a short pulse width. The effect is that echo detectability is enhanced without the resultant increase in noise usually associated with increasing the energy of the pulse.

182 FM Slide Signal Receiver

183 Comparison of CW vs FM Slide Signal on Color Echogram The benefits of CHIRP are most pronounced in mobile surveys in open waters where as high as a 15 db increase in signal to noise may be realized. While still significant, gains in reverberant noise-limited environments, such as at hydropower dams or in rivers, may not be as substantial. Target Strength versus Fish Length Estimation Love (1971), 1977, 1981) has developed widely used relationships for relating target strength to length of fish. Other investigators have developed relationships for various fish species and orientations (Goddard and Welsby, 1986; Haslett 1969; Love 1971, 1977, 1981; McCartney and Stubbs 1971; Nakken and Olsen 1977). Target strength in decibels (db) may be converted to estimated fish length following these methods. For studies where fish are monitored acoustically from above (e.g., mobile surveys of

184 lakes), the dorsal aspect relationship is used. That relationship is: TS = 19.1 * (Log(L) - 0.9) *( Log(f) ) where TS = target strength in decibels, L = length of fish in cm, and f = frequency of transmitted sound (khz). For 200 khz: TS = 19.1 * (Log(L) ) L = 10 ^( (TS )/19.1) A simple table may be constructed: TS db 38 khz 120 khz 200 khz 420 khz The A Constant Scaling Factor The output of echo integration (mean sum squared voltage) is proportional to the average density

185 of the fish monitored. In order to scale this relative output from echo integration (mean squared voltage) to absolute estimates of biomass (or abundance), a scaling factor (called the A Constant or, alternatively, Sigma) must be used. This A Constant scaling factor is dependent on two primary parameters, system parameters and fish parameters. The system parameters include the transmit and receive settings, calibration data, frequency, etc. of the acoustic system used to collect the raw data. The fish parameter quantifies the reflecting properties of the fish monitored. A = 1/ (BCS * Pi * c * BPF * PW * TPL *SG) where all factors are described below. The A Constant will have units of fish abundance/meters cubed Volts squared, assuming BSC values are for individual fish. Since all factors in the A Constant except BCS are typically fixed throughout a survey (at least within a lake or other body of water), it is useful to express the A Constant as two different factors, Afish = 1/BCS and Aequip = 1/all other factors. The Aequip value may be the same for one or more surveys. The Afish value, because it is dependent on backscattering cross section, will be different for each survey and probably each range stratum (e.g., each depth stratum within a lake). Depending on how the data is stratified, it may also be different for different areas within a body of water. Backscattering Cross Section of Fish (BCS) The BSC is a measure of the reflectivity of the fish sampled. Target strength TS and BCS are related. TS = 10 log BCS or BCS = 10^(TS/10) m^2 TS or BCS is best measured in situ, during data collection. It is generally best to use the TS values from the *.RAW files), convert back to BCS, then calculate the average BCS. If in situ measurement is not possible, BCS can be approximated from known fish size data (e.g., obtained from netting) using Love (1981) or the work of others. This is most reliably accomplished for fish acoustically monitored in dorsal (or ventral) aspect, since other aspects are highly variable. Typically, a different average BCS value is used for every integrated depth strata (e.g., every 1 m depth strata). Less frequent is the use of different average BCS values for each transect, or group of transects. When integrating sequences within a transect (e.g., every 1 min), different habitat types may justify stratification by combining the integration and the average BCS values from different sequences from adjacent transects (e.g., from near-shore areas). Pi Pi = Speed of Sound in Water ( c ) The speed of sound in water is a function of primarily water salinity and temperature. In general, the speed of sound in freshwater is approximately 1445 m/sec. In other situations, the work of MacLennan and Simmonds (1992) or Urick (1975) can be consulted. For most applications, the following equation from Kuwahara (1939) provides a close approximation: c = T T^ (S-35) m/sec where T = Temperature in Celsius (C ), and S = Salinity in parts per thousand (ppt). Beam Pattern Factor (BPF) The transducer beam pattern factor (BPF) is provided by HTI for each transducer it supplies. Beam pattern factors generally range from 1.0 E-3 to 8.0 E-3. A typical value for a 15 degree

186 transducer might be approximately 5.3 E-3. Pulse Width ( PW ) The transmit pulse width used during data collection generally ranges from 0.1 to 1.0 msec (= E-3 sec). A typical value might be 0.1 E-3. Transmit Pressure Level ( TPL ) The transmit pressure level is expressed as the RMS transmitted pressure squared re micropascals (upa) at 1 m. TPL = 10 ^ (0.1*SL) (upa)^2 at 1 m where SL = source level of the acoustic system at the transmit power used during data collection. System Gain (SG) The squared through system gain is calculated from calibration data and the echo sounder receiver gain settings used during data collection. SG = 10 ^ (0.1 Gx) (V/uPa)^2 where Gx = Through system gain of the acoustic system used during data collection. This assumes an ideal 20 log R + 2 alpha r TVG. This value must include both the system receiver gain and the TVG gain. Summary Calculation of Aequip An example of a summary calculation using the examples of values above would be as follows: 1 Aequip = = 1 / E3 or E-4 (mv2) * 1445 m/sec * 5.3 E-3 * 0.3 E-3 sec * E20 (µpa)^2 * E-15 (V/µPa)^2 Summary Calculation of Afish Of course, the Afish calculation will probably be different for each depth strata (and sub-area, if stratifying by sub-area) since there will be different mean backscattering cross section (Sbs) estimates for each strata (or sub-area). For example, if for one fish TS = db, then Sbs = 10(-49.0/10) m^2 = E-5 m^2 If you have more than one fish, calculate Sbs for additional fish, then calculate the Average Sbs for all fish. Then 1 Afish = = E4 fish/m^2 Average Sbs Calibration Sheets

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