PAMGUARD User Tutorial 1.2.00, 2 Mb
Contents
1. Energy Sum Minimum Frequency 100 000 Maximum Frequency 200 000 Use log scaled spectrogram Display scaling Vertical scale Factor 0 200000 Peak picking Threshold fi UU Min time over threshold o 00000 Min time before next detection o aaaon Cancel Figure 17 Parameter settings for the energy sum detector example Right click on the spectrogram and choose Settings Select 1 panel and hit enter then go over to the Scales tab There choose a frequency range of 100 300 Hz by setting the min and max frequency and set the amplitude range to 150 170 dB The number of pixels per FFT will depend on the size of your display try 3 to start Next on the Plugins tab make sure the energy sum graphics checkbox is checked Click Ok Now you re ready for Detection gt Start on the menu You should see humpback song units appear in the spectrogram Figure 18 anda detection function appear below the spectrogram The detection function specifies over time the amount of energy in the frequency range you specified 100 300 Hz The threshold you set will cause PAMGUARD to trigger a detection every time the detection function goes over this threshold 19 PAMGUARD V 1 2 00 Tutorial ES FFT 1024 point 1000 0 Hz i O x seconds 0 0 20 0 40 0 60 0 80 0 3002. 170 100 150 Th WE Lk rv LAT US VO Figure 18 Example of the energy sum detector in operation Ex 5 2 Spectrogram Correlation We are going to detect A calls of Atlantic blue whales by using a spectrogram correlation detector First load the sound file blue whale Atlantic wav On the menu choose Detection gt FFT Parameters Figure 20 and set the FFT length to 512 samples the FFT Hop to 256 samples and the window type to Hamming Close this dialog box FFT Parameters X Raw data source For FFT Raw input data From Sound Input 1 jv Channel 0 FFT Parameters FFT Length 512 FFT Hop 256 Window Hamming Figure 19 FFT settings for spectrogram correlation example 20 PAMGUARD V 1 2 00 Tutorial Next choose File Add Modules gt Detectors Ishmael spectrogram correlation and give it the name spectrogram correlation Then choose Detection gt Spectrogram Correlation Settings Figure 20 Sometimes Spectrogram correlation Settings doesn t show up on the detection menu immediately If this happens you can get it either by quitting PAMGUARD and restarting it or by opening File gt Show data model and right clicking on the red bar in the spectrogram correlation box For segment 1 enter O for t0 18 for f0 10 for t1 and 17 for f1 For segment 1 enter 10 for t0 17 for f0 15 for t1 and 15 for f1 Leave the other segments blank and use 1 H
3. Start detection by selecting Detection gt Start from the main menu You are now running PAMGUARD in active mode Ex 3 1 Tracking clicks manually The bearing time display scrolls with time and detected clicks are displayed as ellipses As clicks appear on the bearing time display the Click Detector s side panel display Figure 6 updates the number of clicks detected in the last 10 minutes cdi of Clicks cdl Detections in last 10 minutes V Tracked Clicks cd1 Chicks lg Click Trains Click Train Detector L Click Events 0 Figure 6 Click Detector side panel display Figure 7 Map Panel drop down menu To track detected clicks manually select a click in the Bearing Time display by left clicking on it This will draw a cross on that click to confirm its status as being tracked Next click on the map panel tab to bring forward the map display Using the right mouse button or for Macs hold the ctrl key and click click on the map display to bring up the map detection drawing options This provides a selectable list of items which are suitable for drawing on the map An example is shown here Make sure that Tracked Clicks is selected as indicated by a checkmark v for the Click Detector which you are using in this case Click Detector 1 This will draw the bearing lines for that click on the map panel as indicated in Figure 8 11 PAMGUARD V 1 2 00 Tutorial map cdi g Figure 8 Tracked click bear
4. A User s Introduction to PAMGUARD PAMGUARD Tutorial version 1 2 00 March 2009 PAMGUARD V 1 2 00 Tutorial Contents PANIGUARD OV CIVICW saeco eee ana ee 3 Exercise 1 fastens ANIG WARD x essas33 05 5524505530885 956h955 503 saandeassgasanansous easdeassae anaes Sasa 6 Exercise 2 PAMGUARL TaimillanlS AON siccsaesaceiaresarnsatsarnaiteda tdi iutndetedachaadhdatiea data tech nonsense 6 Ex 2 1 aunchingiP AMG WARD gas53 saahehsgoasahsaahesssasaasasasabsnanssseasdgsaagenansnasesseasansaaoanapanagasseasasasas aoa 6 Ex 2 2 PAMGUARD GULOVErVIEW sister saat heals at eee ict lee tei atone ete E aia a rare eae 7 Ex 2 3 SNE NS A ee E EE E EE EEE 8 Ex 2 4 Setting up a SOUNC SOUICE ccceeccceeccceeeeceeeecee cece eeseueeesaeesseeeseeeesseeesseeesseesseessgeesseeesseeesaaess 9 Exercise 3 Running the Click DeteCtor cccceeccseccceeeceeeceeceueeseeeceeeceuecsueeaaeecseeseuseeueeaeeeseeeseussaeeeaas 10 Ex 3 1 Tracking clicks manually ccccceeccecceeeceeeseeeneeceeeceeeseeeeeeseeeseeeeeeseeeseeseeeseeeseeseeeseeeseeseeeseeeneess 11 Ex 3 2 Tracking clicks automatically cc ccccccceecceeeseeeeeeceeeseeceeeceeeseeceeeseeeseeseeeseeeseeeeeeseeeneeseeeseeeneess 12 Exercise 4 PACING a Spectrogram DISDA sasaa nese ease Saas 14 Ex 4 1 Add plug in displays to the spectrogram xc2cceccescce acide ele edna eieei ed edna eahantateameaie 16 Exercise 5 WY SUCCIC VETOCIO Messrs nina agoasdousdaaadaandundaundaunsansdeuaaouasgananta
5. s set of located calls s Af PAMGUARD V 1 2 00 Tutorial FArFT 512 point 32000 0 Hz joj xj seconds channel 2 Figure 28 Localizing a dolphin whistle the red box indicates the selection to localize Exercise 7 Running the PAMGUARD 3 D module These instructions guide a user on how to configure the 3 D module in PAMGUARD for estimating range and depth of a source using a long aperture towed array At the time of this writing the module has only been tested with synthetic WAV files and not real time input and only with a Static and Threading Hydrophone Locator The instructions begin with an overview of the data model arrangement for the model the preliminary configuration for all upstream modules and a description of the options for the 3 D tracking module itself Two configuration files are available to demonstrate and confirm basic operability 1 Sim3D_wavinput_noGPS_ICltest_Feb2008 psf and 2 Sim3D_wavinput_noGPS_ Cltest_twoanimals_ Feb2008 psf 28 PAMGUARD V 1 2 00 Tutorial The first configuration demonstrates the use of simulated data from a single source while the latter loads simulated data for two sources and which requires an analysis of the inter click interval ICI to correctly assign each pulsive detection across the array Preliminaries lf either configuration file is loaded and Data Model view selected one will see a basic setup for the 3 D tracking Jq Pameguard Data Mod
6. 0 2 20 0 kHz 0 Jo 10 0 dB 15 0 Vp p 0 0 20 0 kHz E 1 1 10 0 dB 5 0 Vp p 0 0 20 0 kHz 2 2 10 0 dB 5 0 Vp p 0 0 20 0 kHz Speed of sound 1500 0 mis Figure 25 Key parts of the hydrophone array configuration for the localization example The Type and Bandwidth fields don t matter here 295 PAMGUARD V 1 2 00 Tutorial Under channel configuration make sure data channel 0 is connected to hydrophone 0 data channel 1 is connected to hydrophone 1 and data channel 2 is connected to hydrophone 2 This is the default so you probably won t have to do anything here Also near the bottom of the dialog box set the speed of sound to 1500 m s Click Ok Next load the sound file dolphin whistle 20 20 wav On the menu choose Detection gt FFT Parameters Figure 26 and set the FFT length to 512 samples and the FFT Hop to 100 samples and the window type to Hamming Click Ok to close the dialog box FFT Parameters x Raw data source For FFT V Ravw input daka From Sound Input T Jw Channel 0 Jw Channel 1 Jw Channel 2 FFT Parameters FFT Length 512 FFT Hop fioo Window Hamming Cancel Help Figure 26 FFT parameters for the localization example Next choose File Add Modules gt Detectors gt Ishmael Locator Results and give it the name Ishmael locator Click Ok Then open the Detection gt Ishmael Location Setti
7. 2 0 Algorithm Block Average Minimum detection interwal s 1 0 Detection Bands End note Signal Band _ In Band Threshold dB Guard Band Threshold dB _ Start Low Frequency Hz End High Frequency Hz Moise Window 3 i Signal window s AEnd note guard Guard Band Associated Signal Band End note _ Start Low Frequency Hz io00 0 __EndjHigh Frequency Hz 1500 0 Moise Window 54 6 0 i Signal Window 5 30 Cr C Figure 52 Likelihood Parameters Configuration Dialog 46 PAMGUARD V 1 2 00 Tutorial Here we are using the Block Average algorithm which is suitable for most situations The signal window is set to 3 0 seconds which approximates the duration of an endnote call with the Start Low frequency set to 100 Hz and End High frequency set to 700 Hz to cover the bandwidth of the call The Noise window is set to 6 0 seconds due to the closely spaced calls The rule of thumb 3 times the Signal Window is not used in this case as the calls only have about a 1 5 second gap between them 3 0 2 x 1 5 6 0 You can define an arbitrary number of configurations each one with multiple signal bands Each signal band can also have multiple guard bands though one on an appropriate side or two skirting the signal band is most appropriate Please read the on line help for more detail and information on how to use a more complex configuration Finally right click on the spectrogram window in the User Disp
8. 3 ol EJ Fie Detection Display User Display Help 12 December 2008 00 41 41 GMT Audio File C Documents and Settings user Deskktopibsa04902 0313 way 4 0kHz 1 channels Idle OOOO File E Figure 44 PAMGuard main window after adding User Display panel Next via the User Display menu select New Spectrogram This will ask you to also add a FFT Spectrogram Engine as a dependency Figure 45 41 PAMGUARD V 1 2 00 Tutorial Module dependencey manager The Spectrogram you are trying to create requires a 2 FFT Spectrogram Engine before it can operate Do you wish bo go ahead and create a FFT Spectrogram Engine Figure 45 FFT Spectrogram Engine Dependency Choose OK to add this module Next you will be asked to provide a name for the new FFT Engine Click OK to accept the default module name Figure 46 Module Name New Module Mame Module name For new FFT Spectrogram Engi FET Spectrogram Engine Set Defaults Figure 46 Naming FFT Spectrogram Engine Dependency Next PAMGuard will show you the Spectrogram Parameters dialog We will need to make changes in the Data Source Scales and Plug ins tabs First in the Data Source tab set the Number of Panels to 1 since we have a single channel wave file making sure to press enter in the text edit box after entering 1 See Figure 51 Spectrogram Parameters _ Data Source Scales Plug ins
9. Peak Peak voltage range 5 00 Preamplifier gain fio 0 dB Bandwidth fio g to 20000 g Hz Figure 4 Sound acquisition configuration dialog Exercise 3 Running the Click Detector The loaded configuration already has a Click Detector plug in added Clicking on the Click Detector module s tab will bring forward the main Click Detector interface panel Figure 5 map cdl Vertical Aids bea FA Bearing Time Display Sele 15 March 2007 15 25 37 GMT Follow Display Seconds 10 0 iy AYU a 4 EFECT ERTO TES Click Waveform Display O X FA Click Spectrum Frequency kHz Figure 5 Click Detector Tab Panel 10 PAMGUARD V 1 2 00 Tutorial The panel has four main components Bearing Time Each detected click is shown as a circle or ellipse on the scrolling display display The toolbar at the top of the display can be used to select the type of vertical axis bearing amplitude or inter click interval Click waveform The waveform of each detected click appears on the display as it is display detected Click spectrum The power spectrum of each click is displayed as it is detected Trigger display The trigger window shows the amplitude of the signal on each channel as a decaying histogram The vertical red line represents the trigger threshold set in the detection parameters dialog cross reference Level meters for each channel are also shown on the right hand side of the trigger window
10. add a Whistle Detector module to PAMGUARD Ensure that Detection mode is not active Detection gt Stop Select File Add Modules Whistle Detector from the main menu The following dialogue will appear if an FFT module is not already included in the configuration Select an Option ka The Whistle Detector you are trying to create requires a FFT Spectrogram Engine before it can operate Do you wish to go ahead and create a FFT Spectrogram Engine Figure 33 FFT Engine creation dialogue Whistle detector modules require spectrogram data to work FFT modules provide spectrogram data and PAMGUARD knows at this point that no FFT data producing modules are present PAMGUARD therefore asks if you would like to make one Click Yes A new dialogue will appear asking you to name the FFT Engine module New FFT Spectrogram Engine i Enter a name For the new FFT Spectrogram Engine A IFFT1 Figure 34 Naming the FFT Engine module In this dialogue enter FFT1 as the name for the new FFT Engine and click OK The next dialogue to appear is for the configuration of the FFT Engine ee PAMGUARD V 1 2 00 Tutorial Channel 0 Channel 1 FFT Length FFT Length 1024 Figure 35 Setting the FFT data source From the drop down data source box select Raw input from Sound Acquisition and make sure that both channels are checked Leave the rest of the parameters as default and click OK Next enter WD1 as the name for th
11. amplitude clicks Again select Detection gt Click Detector 1 gt Detection Parameters from the main menu This time increase the Threshold setting above the default setting of 10 0 dB This will increase the level above the measured background which must be exceeded by clicks to become detection candidates Click OK and observe the Click Detector display Wait for the algorithm to settle down with the new settings up to 10 seconds 50 PAMGUARD V 1 2 00 Tutorial If your setting is too high then genuine clicks may not be exceeding the threshold and the click display will look rather sparse If the setting is too low you will still be seeing the interference clicks Experiment with this setting until you are happy with the results Vertical Axis C Bearing Amplitude gt ICI Bearing lime Display 22 March 2007 13 28 40 GMT a oo a os oh a J i a BE Figure 57 Results of adjusting Click Detector trigger threshold Exercise 12 Don t stop now This tutorial has given you a brief introduction to setting up and using PAMGUARD There are more PAMGUARD plug ins and features for you to try out Here s some ideas to get you going Set up a Sound Recorder module and trigger recordings from click trains Use a decimator to provide lower sample rate data to a second spectrogram Display smoothed spectral data on a spectrogram Try these out with the other example sound data files The PAMGUARD developers
12. are keen to know what you think of the software so any comments good or bad are very welcome Also if you think this tutorial can be improved in any way please let us know at support pamguard org Thanks for taking the time to do this tutorial Hopefully you ve enjoyed this and learned some more about PAMGUARD You can contact us and keep up with PAMGUARD news through visiting www pamguard org 541
13. click train reaches sufficient length and the bearing change is adequate target motion analysis automatically calculates a range and bearing to the sound source The first and last bearing lines associated with this click train Sequence are also automatically displayed on the map An example is shown in Figure 11 13 PAMGUARD V 1 2 00 Tutorial map edd GPS data Latitude Longitude Time Date True Course Speed 07 5 knots Cursor position Latitude 56 05 978 N Longitude 2 43 820 vy Range data Vessel cursar Range 5237m Bearing 78 T Figure 11 Click Train range estimates drawn on the map Note that the lines terminate at the point of bisection indicating the range estimate Now hover the mouse cursor over this point and observe the Vessel cursor range and bearing on the map information panel Take some time to experiment with the Click Detector and map views Try the program with the file SpermSurvey wav a recording made in the course of a real seismic survey from a survey vessel of Australia Select Detection Stop from the main menu to stop the detector Exercise 4 Adding a Spectrogram Display Detections can be viewed in a number of PAMGUARD graphics modules For this exercise you will firstly use a Spectrogram Display Spectrogram Displays are placed on a generic User Display panel so first of all you have to add a User Display panel to PAMGUARD To add the new User Display panel you
14. is useful for range estimation Ex 2 4 Setting up a sound source First of all you will need a source of sound PAMGUARD modules can acquire sound data in a number of ways e g sound can be acquired directly from the system sound card from some other digital acquisition device or sound files can be loaded and re playea In the exercises you will play back sound from a file rather than receive it in through a sound card PAMGUARD will operate in exactly the same way as it would if the sound were coming in through the sound card If a sound playback module is included in the PAMGUARD configuration then analysis will be in real time If a sound playback module is not included then PAMGUARD will process data as fast as possible To load a sound file your configuration must contain a Sound Acquisition module Go to the settings dialog for the sound acquisition module Figure 4 In Data Source Type select Audio File Select the file of choice AIF or WAV format either using the Select File button or selecting a recent file from the drop down list The sample rate and number of channels will be read automatically from the file If you have calibration information you can also enter it here but this is not required for any of the exercises in this tutorial PAMGUARD V 1 2 00 Tutorial Audio Data Acquisition Select File File date Unknown file time Sample Rate 48000 Hz Number of Channels 2 hit enter
15. over the map display If you cannot see this make sure you have selected the map tab panel by clicking on its tab and click on the centre map on ship map control button see table below GPS data are simulated for demonstration purposes Experiment with the map controls which have functions as described below This control pans the map such that the vessel which Centre map supplies PAMGUARD s GPS feed is represented in the on vessel centre of the display by the icon These controls allow the user to zoom in and out of the map Zoom out in view These functions can also be achieved using the mouse wheel Dd These controls allow the user to either measure by dragging Measure Pan the mouse across the display or to pan or drag the display to view a different region Fay ee hy 8 PAMGUARD V 1 2 00 Tutorial Ship North These controls set the map s orientation to ship s heading orientation and North respectively These controls allow the user to rotate the map to a desired Rotatemap arbitrary orientation N UO U Note the information panel at the lower right hand corner of the map This shows useful information such as the position of the vessel which is supplied by the GPS feed to PAMGUARD Move the mouse cursor around the map and note that the Latitude and Longitude of the cursor position is provided and in addition the range from the mouse cursor to the host vessel This
16. something like this Map D1 UD1 f fs 20 Signal Trigger Level dB e Driver 48 0kHz 2 channels Running 0 0 0 0 RRR 0h 0 W M B Figure 54 Click Detector display example for noisy seismic data Notice the rapid click detections associated with the electrical noise on the 90 bearing 49 PAMGUARD V 1 2 00 Tutorial Ex11 2 Adjusting click detection parameters Right click on the Click Detector Bearing Time Display and select Amplitude Time This changes the Y axis of the plot to represent the amplitude of detected clicks Notice that the rapid clicks consistently appear at lower amplitude to the majority of the rest of the click detections Figure 55 If all of the clicks appear at the top of the display you may need to adjust your computer s mixer settings to reduce the amplitude of the captured sound You can also adjust the amplitude scaling of the display by right clicking and invoking the settings dialog Bearing Time Display Sel 22 March 2007 13 16 30 GMT Seconds 10 0 Click Display Parameters Axis Click Size oa TPR pe Bearing Amplitude ICI Maximum ICI 5 Amplitude Range 60 0 to 160 0 dB Horizontal grid lines 0 Heb Set defeats _ Figure 56 Adjusting the amplitude scaling for the Click Detector Amplitude display We will now adjust the click trigger threshold such that the Click Detector will not trigger for these lower
17. the 100 300 Hz frequency band First load the sound file humpback whale example wav a recording of a singing humpback whale On the menu choose Detection gt FFT Parameters Figure 16 and set the FFT length to 512 samples and the FFT Hop to 256 samples Close this dialog box FFT Parameters x Raw data source For FFT Raw input data From Sound Input 1k Jw Channel 0 FFT Parameters FFT Length 512 FFT Hop 256 Window Hamming Cancel Help Figure 16 FFT parameter settings for the energy sum example Choose File Add Modules gt Detectors gt Ishmael Energy Sum and give it the name energy sum Next choose Detection gt Energy Sum Settings Figure 17 Sometimes Energy Sum Settings doesn t show up on the detection menu immediately If this happens you can get it either by quitting PAMGUARD and restarting it or by opening File gt Show data model and right clicking on the red bar in the energy sum box Set the minimum frequency to 100 Hz the maximum to 300 Hz and uncheck the Use log scaled spectrogram box if it s checked Also set the vertical scale factor to 0 2 and the threshold to 1 5 The data source at the top should remain Basic FFT Close this dialog box 18 PAMGUARD V 1 2 00 Tutorial Energy Sum Parameters x Data Source 7 Basic FFT 1024 pt FFT Jw Channel 0
18. which the spectrogram displays spectral amplitude data Repeat this until you are happy with the view For the sound file you have running at the moment you should see regular whistle contours as in the image above Now right click over the top panel on the spectrogram display and this time choose Spectral Peak Blocks Small blue rectangles will now be overlaid on the channel 0 panel on top of peaks detected in the sound spectra These peaks are candidate components for whistles Where consecutive peaks are connected in such a way as to satisfy the Whistle Detector criteria a whistle detection is created Now right click over the lower panel on the spectrogram display and this time choose Whistles 34 PAMGUARD V 1 2 00 Tutorial EB Raw FFT Data DAR re K z g yenir ia ie PeR p y A 7 i 4 m rae _ k 2 oe T dl Ee as Bel wie Rese obs Bt a p r g ie canes FT ik E a Fa chann Figure 23 Spectral peaks and whistle detections on spectrograms As is illustrated in the figure above detected whistles will now be overlaid on the panel as coloured lines which track the detected whistles Ex 8 4 Data from Seismic Surveys Try running the whistle detector with recording made during seismic mitigation exercises File whistlesurvey wav Was made from a seismic source vessel off Australia with electrical gating of the airgun pulse The whistles come from a bottlenose dolphin File whistle
19. Mark Observers Source Data FFT 1024 paint 4000 0 Hz FFT Spectrogram Engine 1024 pt FFT wt FFT 1024 point 4000 0 Hz 0 Number of Panels 1 hit enter Panel 0 channel D w FFT Length 1024 samples FFT Hop 512 samples Sample Rate 4000 0 Hz Figure 47 Spectrogram Parameters Data Source tab 42 PAMGUARD V 1 2 00 Tutorial Next on the Scales tab set the min and max Amplitude Range as shown in Figure 48 These parameters are used to set the image quantization levels on the resulting spectrogram That is 110 dB and lower is drawn as white and 170 dB and higher is drawn as black with shades of grey in between Spectrogram Parameters Data Source Scales Plug ins Mark Observers Frequency Range Min Hz Default 2 Default Max 2000 Amplitude Range Min Max Colour model Grey black white Time Range Pixels per FFT Window length is as 5 Figure 48 Spectrogram Parameters Scales tab Finally on the Plug ins tab check the Raw input data from Sound Acquisition box Figure 49 Checking this will add a view of the raw input data samples on a separate plot underneath the spectrogram When you are finished click the OK button 43 PAMGUARD V 1 2 00 Tutorial Spectrogram Parameters Data Source Scales Plugins Mark Observers Select additional display panels _ FFT Spectrogram Engine Spectra Figure 49 Spectrogr
20. am Parameters Plug ins tab After configuring the spectrogram parameters an empty spectrogram window will be displayed in the User Display panel Figure 50 FFT Spectrogram Engine 1024 pt FFT Sel seconds 0 0 2000 channel 0 o 1 0 Raw input data from Sound Acquisition Figure 50 Empty Spectrogram Window 44 PAMGUARD V 1 2 00 Tutorial Next we will configure the FFT Engine which produces the spectrogram s data From the Detection menu select FFT Parameters Set the FFT Length to 512 and the FFT Hop to 256 Figure 51 These settings are adequate for viewing the whale calls we will be processing Click OK FFT Parameters Channel 0 FFT Parameters FFT Hop 256 Figure 51 Configure FFT Spectrogram Engine Ex 10 5 Configure the Likelihood Detector s Parameters Now we will set up the detector itself From the Detection menu select Likelihood Detector which will display the configuration dialog You will next need to add a configuration by right clicking on Target Configurations and selecting Add configuration You will need to name the new configuration Since we are configuring for a Bowhead whale name it Bowhead Expand the Bowhead configuration by pressing the widget next to its name and add a signal band by right clicking on the Detection Bands and selecting Add Signal Band Name it Endnote Now expand the Detection Bands and Endnote Sig
21. art up Browse Cancel Figure 1 PAMGUARD configuration dialogue This dialogue allows the user to choose from the selection of PAMGUARD configuration files available on your system Press the browse button and navigate to where you ve stored the sample configuration files Select the appropriate configuration file and click OK In this case this will be PAMTutorial1 psf The first time you run PAMGUARD on a new machine you will have to press the Browse button and search for the psf file After that recently used files will be stored in the drop down list When OK is clicked the dialogue will disappear and the PAMGUARD application will launch During the launch the following dialogue may appear 6 PAMGUARD V 1 2 00 Tutorial Set PC Clock Current PC System Time 15 March 2007 12 08 26 GMT Current GPS Time 15 March 2007 12 08 25 GMT Auto set on Pamguard start up site Figure 2 Set PC Clock Dialogue You should ignore this dialogue for this tutorial After a few seconds it will disappear In real operation this would synchronise your PC clock with the time provided by the GPS system Ex 2 2 PAMGUARD GUI overview Once launched the PAMGUARD Graphical User Interface GUI will look something like Figure 3 a pep p PamGuard HH Tee oa 754 N jLongitude 2 59 922 w 02 December 2008 170 0 T 75N Latitude 55956 533 N Longitude 2047 946 W Bearin
22. bySound file earlier Figure 42 39 PAMGUARD V 1 2 00 Tutorial Audio Data Acquisition Data Source Type Audio File w Select sound File C Documents and Settings useriDesktop BS6041902 03135 weay Select File File date Sampling Sample Rate oo O Hz Mumber of Channels 1 Chit enter Calibration Peak Peak voltage range Preamplifier gain dE Bandwidth to z i Cancel Figure 42 Configuring the Audio Data Acquisition The default settings are appropriate so press the OK button when finished Ex10 4 Adda Spectrogram Display Here we will add a Spectrogram display so that you can see a gram of the audio file being played back Please note this section does not affect the Likelihood detector s performance and the detector can be used without a spectrogram However it is often useful to see the spectrogram and the detection events drawn as overlays First we must add a User Display Panel Do this by navigating to the File gt Add Modules gt Displays menu and select User Display Panel Click OK on the default name Figure 43 40 PAMGUARD V 1 2 00 Tutorial Module Name x Module name For new User Display panel User Display panel Co _ Set Defaults Figure 43 Naming the User Display panel This should add a new tab to the main PAMGuard window as well as a menu item entitled User Display The main window should now look similar to Figure 44 pa PamGuard
23. ched Filter Settings doesn t show up on the detection menu immediately lf this happens you can get it either by quitting PAMGUARD and restarting it or by opening File gt Show data model and right clicking on the red bar in the matched filter box In the kernel sound file area click Select another file and choose the file blueDemo NEPac kernel wav Set the vertical scale factor for the display to 500 and the threshold to 0 0004 Click Ok to close the dialog box Matched Filter Parameters X Data Source Raw input data From Sound Input 1 ha Jw Channel 0 gt Matched Filter Kernel sound File C blueDemo NEPac kernel way Select another Fi Display scaling Vertical scale Factor fn mPeak picking Threshold 0 0004 Min time over threshold o o0000 O Min time before next detection pooo Figure 23 Parameter settings for the matched filter example 23 PAMGUARD V 1 2 00 Tutorial Right click on the spectrogram and choose Settings Select 1 panel and hit enter then go over to the Scales tab There choose a frequency range of 10 60 Hz by setting the min and max frequency and set the amplitude range to 80 110 dB The number of pixels per FFT will depend on the size of your display try 1 to start Next on the Plugins tab make sure the matched filter graphics checkbox is checked Click Ok to close the dialog box Now you re ready for Detection gt Start on
24. cotaanioansoate 17 Ex 5 1 Energy SUM DeleCIOi aie ee E 18 Ex 5 2 Spectrogram Correlation ccccceccccsecccsececeeeeceeeeceueeceuceseeeeseeeeseeeeseueeseueeseueeseueeseueeseuseseueesaes 20 Ex 5 3 Matched filter Detector ccccccceecceeccceecceeeceueceueeaeeeseeeceuecsuecsueeceeesaeesuecsueeseeeseeeseeeseuesseeenes 22 Exercise 6 Ishmael hyperbolic localize eee cceccceeccececeeeceeeceeeeaeeseeeceueeeeeeseeeseeseueeaeeeseeeseeeseueeeeeenes 25 Exercise 7 Running the PAMGUARD 3 D module ccccccc cece eeeceeeeeeeeee cena eeseeeseueeeeeeaeeeseeeseueeaeeenes 28 Exercise 8 TRAV eV TUS UNS IES Ee UO erst aoc tata ahceestnrcterceecr a ect areca acct cece een et eae tendeandma eM MaNaNe 32 Ex 8 1 Load INE SOUMC TING a seas aist ate aah ash ashe a anh 55S as wae saga a gyaaenaasnanaaaasaaeae 32 Ex 8 2 Adading a VWiniStie Detector Module nuit eee E E 32 Ex 8 3 VIEWING WSUS CETECUONS sssi EN 34 Ex 8 4 Data nom Seme SUVEST ER E ae 35 Exercise 9 Advanceddisplay TE ATURCS i328 ook cook chat hah oh he ee oe atc acetone oan aaee Ahan ata aA athe 35 Ex 9 1 Adding further displays to Spectrogram Panels ccccccccseeeceeeeeeeeeeseesseeeeseeeeseeeeseeesaeeesaaees 35 Ex 9 2 Adding a Radar Display to the User Display panel cccccccececeeeeeeeeeeseeeeeeeeeeeeaeeeseeeseeesaees 36 Exercise 10 Likelihood Detector cece cece ceccceeeceeeeeeeeaeeeceeeseeeeeueeseeeseeeseueeeueeseeesaeeseueeeeeeseeeseeeseueeeneene
25. cting Settings Ex 4 1 Add plug in displays to the spectrogram Many PAMGUARD modules have plug in displays which attach to the bottom of the spectrogram displays Right click on the spectrogram to access the spectrogram configuration dialog Go to the Plug ins Tab Figure 15 and select one or two of the available plug in displays Start detection and you will see additional display units at the bottom of the spectrogram display Some plug ins have additional options which can be accessed by right clicking on specific plug in panels 16 PAMGUARD V 1 2 00 Tutorial Spectrogram Parameters x Select additional display panels l Raw input data from Sound Acquisition F Click Trigger Function M Click Detector CD1 l Filtered Data from CD1 FFT Spectrogram Engine Spectra Cancel Help Figure 15 Spectrogram plug ins configuration Exercise 5 Mysticete Detection This set of exercises will demonstrate three different detectors which have been ported to PAMGUARD from Dave Mellingers Ishmael software Energy sum Spectrogram Correlation Matched Filtering The energy sum detector takes a spectrogram and sums the energy in a given frequency band It s sensitive to any sounds in that frequency band and would not for example be able to tell the difference between an upsweep and a downsweep Energy sum detectors are extremely simple but are good for making a first pass through a data set highlighti
26. e Whistle Detector module New Whistle Detector Enter a name For the new whistle Detector A wD Figure 36 Naming the Whistle Detector module Click OK Access to the Whistle Detector settings is from the main menu Detection gt Whistle Settings The Whistle Detector will also place an item on the side panel as shown in Figure 37 Now that you have changed the PAMGUARD model configuration click File gt Save configuration as and save the configuration as clickAndWhistleDetectors psf WWD Detections in last 10 minutes Whistles Whistle Events a Figure 37 Whistle detector side panel display Close down PAMGUARD File gt Exit and re launch the application Choose clickAndWhistleDetectors psf from the Load PAMGUARD configuration from dialogue and click OK 33 PAMGUARD V 1 2 00 Tutorial Note This closing down operation is not necessary for PAMGUARD to operate with the new configuration it s just to give you practice Ex 8 3 Viewing whistle detections Start detection Detection gt Start and the two spectrogram panels will show the spectrogram data in real time seconds channel 0 channel 0 Figure 22 A Spectrogram panel display Right click over the spectrogram display and choose Settings from the menu Now click on the Scales tab Experiment with the spectrogram display by adjusting the amplitude range settings and clicking OK This changes the range over
27. e and bearing information to detected sounds To add the Radar Display to the User Display panel User Display 1 select the User Display 1 tab on the tab panel selector Select User Display gt New Radar display from the main menu since many detectors particularly those using simple linear hydrophones produce ambiguous bearing information it is possible to display either the full display or only one half of the display We will display a half display called RD1 so type in the name and select Right half only from the Style option drop down list Once the Radar Display is on User Display 1 select User Display gt Arrange Windows gt Tile Vertical from the main menu The display should look something like Figure 36 PAMGUARD V 1 2 00 Tutorial Figure 25 A Radar display added to the User Display Panel Right click over RD1 and choose Settings gt Detectors From the Detectors tab select the Show Detector Data settings as indicated in Figure Radar Display Parameters PAREA Scales Detectors Show Detector Data Detector Lifetime s Clicks 1 Tracked Clicks 20 Whistles 1 Figure 26 Detector selection and lifetime settings for Radar Display Click OK This will set the radar plot to display Clicks Tracked Clicks and Whistle detections for 1 20 and 1 seconds respectively Experiment with the plot settings and when you have finished select Detection gt Stop from th
28. e main menu in preparation for the next exercise Exercise 10 Likelihood Detector The likelihood detector module is an implementation of a detector based on the likelihood ratio test LRT It is suitable for detecting both short duration Odontocete clicks Sperm Beaked etc as well as moderate duration Mysticete calls Humpback Bowhead eic It is not suitable for detecting whistles For an optimized whistle detector please refer to Exercise 8 This example assumes you are beginning with a new PAM uard session and there are no modules configured It will walk through setting up the Data Source the Detector itself as well as a User Display with a spectrogram widget that will render the raw input data and show the detection events as an overlay This tutorial uses a pre recorded WAVE file from MobySound http Avwww mobysound org which provides many reference recordings From the mysticetes section please download the Bowhead Whale set and extract the file B88041902 0313 wav placing it in a location 87 PAMGUARD V 1 2 00 Tutorial you can easily find later such as the Desktop Once you have the file saved you are ready to proceed with the following steps Ex 10 1 Disable Multithreading Model At the time of writing the new threading model does not work correctly with the Likelinood Detector Select Multi threading trom the Detectionmenu and disable Multi threading Figure 38 Threading Model Select Model Type Mul
29. el Map Comments 0 0 Raw input data from Soundin 40 Sound in Click Detector Tracked Click localisations 0 0 0 FFT Spectrogram Engine 1024 pt FFT faro 3D Towed Array localizer 0 0 3D Towed Array localizer fi Figure 29 Data Model view of demo 3D tracking configuration file Sim3D_wavinput_noGPS I Cltest_Feb2008 psf At a minimum the 3D Towed Array module requires an upstream Data acquisition module and a Click module labelled Sound in and Click Detector in Figure 29 At present the 3D module is configured to only work with the Click Detector and not any Ishmael detectors A typical array configuration is illustrated in Figure 30 which appears under the Hydrophone display At present only two pairs of hydrophones 4 phones total are used in the module 29 PAMGUARD V 1 2 00 Tutorial Pamguard hydrophone array Hydrophone positions Array Configuration Ji Basic Linear Array w C Static array Towedarray Locator Threading Hydrophone v oa va Q a 9 2 Add i 3 Bae Channel Configuration 261 0 Data Channel Hydrophone Gain Bandwidth 0 10 0 dB 5 0 Vp p 0 0 20 0 kHz 3 8 I Hydrophone numbers ADC channel numbers 461 0 l r Environment 159 0 41 0 x m Speed of sound 1500 0 mjs gt Array Management Lee Cancel New Array Copy Rena
30. emented to avoid harm Visual observations play a vital role but marine mammals are difficult to soot on the sea surface especially when weather and light conditions are poor However many marine mammals produce loud and distinctive vocalisations which can often be detected more reliably than visual cues For these species passive acoustic monitoring PAM offers an effective means of detection Furthermore the creatures do not need to be on the surface to be detected A basic PAM system consists of a number of hydrophone elements analogous to microphones in air but used for underwater sound arranged to form an array hydrophone signal conditioning amplification a signal acquisition device e g a sound card anda computer running PAM software Sounds in the water are converted by the hydrophones into electrical signals which are conditioned appropriately and converted into digital signals for processing by the PAM software The PAMGUARD project was set up to provide a standard software infrastructure for acoustic detection localisation and classification for mitigation against harm to marine mammals and for research into their abundance distribution and behaviour PAMGUARD is open source Passive Acoustic Monitoring PAM software based on a platform independent Windows Mac or Linux flexible modular architecture This architecture makes it relatively straightforward to incorporate new modules as they are developed to include addi
31. f the width of the noise window or 3 seconds Since the wave file we have selected finishes before this condition is met the last detection cannot be finalized This is a side effect of using a pre recorded wave file 48 PAMGUARD V 1 2 00 Tutorial It is also worth noting that this detector does not identify and isolate entire events The overlay boxes in blue show the time period when the detector is above the detection threshold and will not necessarily surround the entire event as shown on the spectrogram Exercise 11 Detection during seismic source operation Ex 11 1 Loading the sound file First load the sound file soermWhalesPlusSeismic wav This is a recording of soerm whale vocalisations taken during an active seismic survey The presence of a significant sound source such as firing air guns has implications for the operation of detection algorithms You will notice an artefact on the central axis indicting no time delay between channels This is noise picked up after the seismic pulse which has been gated out Here we will investigate changing the Click Detector settings in an effort to reduce the adverse effects of the unwanted noise select Detection gt Click Detector 1 gt Detection Parameters from the main menu Click on the Set defaults button to restore the detectors settings to their default values start Detection Detection gt Start and observe the Click Detector tab panel displays You should see
32. g 115 7 T Range 13771 m re Latest GPS Data Figure 3 PAMGUARD Graphical User Interface s7 PAMGUARD V 1 2 00 Tutorial The GUI is subdivided as described in the following table Menu bar This provides access to many PAMGUARD settings and controls as well as access to the help system PAMGUARD has a dynamic menu bar system whereby the menu items change according to the current view and settings Clock display Shows the current time Side panel The side panel gives quick access to information and controls for currently active modules Tab panel Tab panels provide access to the main visual interfaces of many of the PAMGUARD modules In this example the map tab panel is shown which consists of a map compass and some GPS data etc status bar This bar provides information on the current status of PAMGUARD e g whether it is running or idle Spend some time investigating the user interface Ex 2 3 Using the map At this point PAMGUARD should be running with the PAMTutorial1 psf configuration Check that this is the case by selecting File gt Load Configuration This will open the configuration dialogue The current configuration will be selected in the drop down list If this is not PAMTutorial1 psf locate and select it Otherwise click Cancel PAMGUARD can run in simulated or real GPS modes In the tutorial configurations the GPS is simulated and the vessel icon will appear on and move
33. ing lines plotting on the map panel Ex 3 2 Tracking clicks automatically The Click Detector can automatically detect sequences of clicks on a consistent bearing with a consistent inter click interval Clicks that satisfy these constraints are referred to as Click Trains To enable this feature select the Click Detector tab panel Then select Click Detection gt Click Train Identification from the menu bar This will bring up the following dialogue Set Defaults Figure 9 Click Train Identification Dialogue Click on the Run Click Train Id check box and select OK Now look at the Bearing Time display Identified click trains are indicated by coloured Note that access to the same dialogue is also possible by selecting Detection gt Click Detector Name gt Click Train Identification from the main menu where Click Detector Name is the name given to the particular Click Detector module running For this exercise this will be Click Detector 1 PAMGUARD V 1 2 00 Tutorial ellipses as in the Figure 10 map cdi Vertical Axis Bearing Amplitude C ICI Bearing Time Display 20 March 2007 11 52 56 GMT w0 2 0 Figure 10 Click trains plotted on the bearing time display Now switch to the map view Position the mouse somewhere on the blue map area and press the right mouse button to display the drop down detector selection box and make sure that Click Trains is selected lf a
34. lay panel and check the Likelihood Detector Bowhead item in the context menu This instructs the spectrogram to draw detection boxes which are generated by the likelihood detector If we had multiple configurations defined in the Likelinood Detector module there would be an item for each one in the context menu Ex 10 6 Play back data file and view detections Now that we have configured the modules select Start from the Detection menu After a short while the file will have been processed to completion and you should see something similar to Figure 53 47 PAMGUARD V 1 2 00 Tutorial EN FFT 512 point 4000 0 Hz FFT Spectrogram Engine seconds 9 0 channel 0 es i d i IP rie p Hie ny AANE Me a DN i ARU wit Bin ni ah COM tid Sea tf ete i i I i fi ae Ni a it hi i AWG o ir i if i A nes ie i ik i y f I i pii wid nee AIS ts i 1LF ai cere ta d T br TH 7 Li a I P Tha Oh i we i 14 At i J gi held Pas I E 1 r Ee i i r 2 Ai kiti i KE PR atl p h pe Paik dh Hint ae a sae ae Hii i Ni va i w i g oes PATE DN Ay i Ta ma ila i fugt Raw input data from Sound Acquisition Figure 53 Processing results of the Likelihood Detector As shown the detector has successfully detected six discrete endnotes in the frequency range 100 700 Hz It is not able to detect the seventh endnote as the block average algorithm requires data to look ahead by half o
35. me Import Export te Figure 30 Hydrophone array configuration Figure 31 shows the configuration menu for the Audio Data Acquistion module Soundin in Figure 44 should be configured to select a synthetic wav file either test3D_azi45 R566m wav for a single simulated source or test3D_azi45 R566m_multanimals wav for two sources The wav file has 4 channels with the hydrophone closest to the tow vessel being assigned the lowest channel Audio Data Acquisition Data Source Type E Select sound File C Documents and Selfiga Thode My Documents Projects PAMGUARD SeriaIPort 3D_Tracker test3D_azi45_R566m_multanimals wav Select File File date Unknown File time Sampling Sample Rate Number of Channels p hit enter Select Channels Panel 0 channel lo Panel 1 channel lo K Panel 2 channel o Panel 3 channel lo Peak Peak voltage range 5 00 Preamplifier gain 10 0 dB Bandwidth 10 0 to 2000 0 Hz Cancel Figure 31 Settings window for importing simulated WAV data The exact file path would need to be adjusted before starting the program 30 PAMGUARD V 1 2 00 Tutorial The Click Detection module has many options but only the following menu needs to be changed from the default Figure 32 Click Detection Parameters x Source Trigger Click Length Raw Data Source Raw input data From Sound in Channel list and g
36. n function specifies over time the degree of match between the spectrogram and the frequency contour you ve defined By setting a threshold in this function you cause PAMGUARD to trigger a detection every time the detection function goes over this threshold FA rrt 512 point 100 0 Hz O Bije Es seconds 0 0 100 0 200 0 300 0 400 0 aq I 180 160 spectrogram correlation graphics Figure 21 Example of blue whale call detection using spectrogram correlation Ex 5 3 Matched filter Detector We are going to detect calls of northeast Pacific blue whales by using a matched filter detector First load the sound file blue whale NE Pacific wav On the menu choose Detection gt FFT Parameters Figure 22 and set the FFT length to 1024 samples and the FFT Hop to 512 samples and the window type to Hamming These parameters dont affect the matched filter which operates on the time domain sound signal but they do make the spectrogram show the blue whale calls well Click Ok to close the dialog box 22 PAMGUARD V 1 2 00 Tutorial FFT Parameters Raw data source for FFT FFT Length i024 FFT Hop 512 Window Hamming Cancel Help Figure 22 FFT parameters for the matched filter example Next choose File Add Modules gt Detectors gt Ishmael matched filtering and give it the name matched filter Then choose Detection gt Matched Filter Settings Figure 23 Sometimes Mat
37. nal Band tree widgets by clicking on the next to their names Note Common default values are used when you first create a configuration or signal band so only custom parameters need to be set If you hover over an item in the window the limits for that parameter are indicated in a tool tip For some parameters these limits will change depending on other parameters In the Endnote Signal Band configuration set the values of In Band Threshold dB End High Frequency Hz Noise Window s and Signal Window s You can edit the values by double clicking them Set them to the values shown in Figure 52 45 PAMGUARD V 1 2 00 Tutorial Similarly add a guard band by right clicking on Detection Bands and configure it s Start Low Frequency Hz End High Frequency Hz Noise Window s and Signal Window s as shown in Figure 52 Note You will see that the Noise Window and Signal Window length are the same for both the signal band and guard band This is intentional and recommended for most cases when guard bands are used For more information see the online help Make sure that the Bowhead configuration is checked to enable it then press the dialog s OK button Likelihood Detector Parameters Raw Data Source Raw input data From Sound Acquisition ka Channel 0 Value 5 Bowhead Time Resolution s 0 1 __ Frequency Resolution Hz
38. ng areas that deserve closer scrutiny Low Processor Gain Spectrogram correlation also uses the output of a spectrogram but rather than simply adding the energy in a given frequency band the spectrogram image is convolved with multiplied by a spectrogram image of a sample sound The closer the match of the image to the sample sound the higher the detector output Spectrogram correlation detectors should be able to tell the difference between an upsweep and a downsweep Moderate Processor Gain A matched filter uses the raw data which is convolved by a template of a sample sound The better the match of the sample sound the higher the detector output Matched filters are in fact the optimal solution for the detection of a known signal in random Gaussian noise However if the template is not an exact match they perform poorly High processor gain To start this series of exercises exit PAMGUARD then restart it and load up the configuration file PAMTutorial2 psf This contains a basic configuration containing a sound acquisition module which will read the sound files FFT Engine and a spectrogram display During the exercises you will add the three detectors and then run them ona variety of sounds A Map and playback module have not been included but feel free to add them if you wish 17 PAMGUARD V 1 2 00 Tutorial Ex 5 1 Energy Sum Detector We are going to detect units in the humpback song by summing the energy in
39. ngs dialog box and make sure the number of dimensions is 2 Click Ok Next right click on the spectrogram and choose Seitings Under Number of Panels type 3 and press the Enter key on your keyboard On the Scales tab Figure 27 left set the frequency range to 5000 16000 Hz with the min and max frequency and the amplitude range to 130 160 dB The number of pixels per FFT will depend on the size of your display try 2 to start Next click the Mark Observers tab Figure 27 right and make sure the Ishmael Locator box is checked Click Ok to close the dialog box 96 PAMGUARD V 1 2 00 Tutorial Spectrogram Parameters xX Spectrogram Parameters x Data Source Scales Plug ins Mark Observers Data Source Scales Plug ins Mark Observers Frequency Range min r Default max fiso Default Amplitude Range 130 0 dE Select spectrogram mark observers M Ishmael Locator Time Range f Pixels per FFT 2 b Window Length is o s Cancel Help Cancel Help Figure 27 Spectrogram parameter settings for the Ishmael localization example left Scales tab right Mark Observers tab Now you can do Detection gt Start You should see a dolphin whistle displayed in 3 spectrogram panels To locate a call the whistle in this case simply use the mouse to draw a box around the call or a part of the call Figure 28 The location will be computed and installed in PAMGUARD
40. ram smoothing Spectrogram displays Radar displays Click Detector Whistle Detector Energy Sum Detector Spectrogram Correlation Detector Matched filter Detector Database interface requires MySQL or MS Access Source simulation An up to date list of PAMGUARD modules can be found at http www PAMGUARD org modules shtml Online Help PAMGUARD has extensive online help which is available from the Help Menu once you ve started PAMGUARD As you go through the exercises you may also want to refer to these help pages Please note that the help system was extensively updated in early 2009 PAMGUARD V 1 2 00 Tutorial Tutorial Learning Outcomes The purpose of this tutorial is to provide a basic overview of how to use PAMGUARD including adding and configuring plug in modules The main learning outcomes are Loading and running PAMGUARD configurations Navigating the Graphical User Interface GUI Basic Map familiarisation Running and configuring a Click Detector module Adding and configuring User Display panels Using Ishmael modules for Energy Sum Spectrogram Correlation and Matched Filter detectors Overlaying detector graphics on display panels Adding and configuring FFT Engines Adding configuring and running a Whistle Detector Adding and configuring a Likelihood Detector These learning outcomes can be achieved through a series of exercises that now follow The exercises can be seen as a guide so you re enco
41. rouping Auto Grouping Channel Group f No grouping Iw Channel 0 C One group iw Channel 1 fe User groups We Channel 2 little lw Channel 3 Cancel Help Set Defaults Figure 32 Detection Parameters Settings Dialog for Click Detector module arranged for two two element subarrays All other parameters are default The Source tab arrangement shown here assigns the first two channels to Group 0 thus generating a forward subarray bearing and the last two channels to Group 1 generating the rear subarray bearing Thus to summarize after downloading the 3DInstruction zip package and opening PAMGUARD do the following steps 1 Load one of the configuration files psf 2 From Data View select properties of Soundin Module and Browse for the example WAV file in 3DInstructionFolder 3 Open the Hydrophone Display and import the BasicLinearArray paf 4 Check settings in 3D localizer make sure Generate 3D positions is checked and choose TOA and rear bearing estimate TOA using ICI 5 On Map view right click on screen and select SD array localizer Bi PAMGUARD V 1 2 00 Tutorial Exercise 8 The Whistle Detector Ex 8 1 Load the sound file To experiment with the whistle detection in PAMGUARD load the sound file whistles wav Start from the settings file used for click detection PAMTutorial1 psf Ex 8 2 Adding a Whistle Detector module Next we will
42. s 37 Ex 10 1 Disable Multithreading Model c ccccssccceecceecceeceeecceeeceeeceuecsueesececaeesueseueeeeeeseeeseeesaues 38 Ex 10 2 Add a Likelihood Detection Module cccccccseccceeeseeeseeeeeeeeueeeceeeceeeeeueeseeeseeeseeeseueeaeeenes 38 Ex 10 3 SOM GUE the Sound AG CUMS UE ON scree etcetera heated 39 Ex 10 4 Adda SPEC OCraml OIS Play kets os eee eee 40 Ex 10 5 Configure the Likelihood Detector s Parameters cccsscceeeceeeceeeceeeeneeeceeeseueceueeaeeeneeens 45 Ex 10 6 Play back data file and view detections sisi aces8cnsiee ceded an eee eee 47 Exercise 11 Detection during seismic source operation cccecccecceecceecceeceeceecceeceueceeeceeseeseeeneeseeeeas 49 Ex 11 1 Loading UNS Sound TING serere aaa E E E E ERR 49 Ex 11 2 Adjusting click detection parameters ccccceeccseceseeeceeeseueeeeeeseeseeeceueeeueeseeeseeeseeeseueeaeeeaes 50 Exorcse T2 DON SIO NOW sirrane 51 www pamguard org PAMGUARD V 1 2 00 Tutorial PAMGUARD Overview Many marine activities involve underwater sound emissions These may be a by product of the activity e g piling or explosives or a tool e g air guns used for seismic surveys in oil and gas exploration or military commercial sonar To mitigate against harm to marine mammals observers are often employed to visually scan the sea surface for the presence of animals In the event of a sighting procedures such as suspension delay of activities may be impl
43. sguard wav was made from a guard vessel during a seismic survey on the Atlantic Frontier Exercise 9 Advanced display features There are a more display types available in PAMGUARD which will be explored here Ex 9 1 Adding further displays to Spectrogram Panels It is often useful to view multiple data and detection types simultaneously For example various detector modules active in PAMGUARD can draw detections on the Spectrogram panels While detection is running right click over a spectrogram panel and choose Clicks Detected clicks will now be plotted on the panel as red circles on the top of the plot 35 PAMGUARD V 1 2 00 Tutorial In addition plots can be added to the bottom of the Spectrogram panel Right click over the spectrogram display and choose Settings from the menu Now click on the Plug in tab Select additional plug in display panels by clicking on the check boxes for Raw input data from Sound and Click Detector gt Click Detector 1 Click OK FFT 1024 point 48000 0 Hz Click DeGctor Ce Ps wy Figure 24 Raw data and Click Detector plugin panels added to a spectrogram display As illustrated in the figure above the raw sound waveforms are plotted and also a compact version of the Click Detector display is shown Ex 9 2 Adding a Radar Display to the User Display panel We will now add a Radar type display to the User Display Radar display windows can be used to display range amplitud
44. te Do you wish to go ahead and create a FFT Spectrogram Engine Cancel Figure 13 FFT Engine creation dialogue 15 PAMGUARD V 1 2 00 Tutorial Click Ok to create the FFT module and Ok again to set the module name or enter a different one The Spectrogram configuration dialog will then appear Spectrogram Parameters x rSource Data FFT 1024 point 48000 0 Hz FFT Spectrogram Engine 1024 pt FFT FFT 1024 point 48000 0 Hz 0 Number of Panels 2 hit enter Panel 0 channel lo kal Panel 1 channel fo kal FFT Length 1024 samples FFT Hop 512 samples Sample Rate 48000 0 Hz Cancel Help Figure 14 Spectrogram configuration dialog Enter 2 in the number of panels box Hit the Enter key on the keyboard to confirm the value and select channel 0 and 1 from the two channel selection drop down lists Click OK and the new Spectrogram Display will appear on the User Display 1 panel The FFT Engine will appear in the model view Figure 12 connected to the sound acquisition module Start the detectors again and you will see a spectrogram scrolling across the screen sperm whale clicks will appear as vertical lines along the display You may wish to experiment with different FFT lengths and other parameters in the FFT Engine configuration dialog The spectrogram configuration dialog shown in Figure 14 can be accessed by right clicking anywhere on the spectrogram display and sele
45. the menu You should see blue whale calls appear in the spectrogram and a detection function appear below the spectrogram The detection function specifies over time the degree of match between the spectrogram and the kernel sound you ve chosen You can set a threshold in this function and have PAMGUARD trigger a detection every time the detection function goes over this threshold ES FFT 1024 point 249 0 Hz 2 oO x seconds 80 matched filter graphics Figure 24 Example of a matched filter detecting calls of northeast Pacific blue whales 24 PAMGUARD V 1 2 00 Tutorial Exercise 6 Ishmael hyperbolic localizer You are going to locate a dolphin whistle using multiple hydrophones First tell PAMGUARD the positions of your hydrophones via File Hydrophone array Figure 25 Under Array configuration at the top choose Basic Linear Array and just below that choose Static array Next using the Add and Edit buttons a bit farther down set up 3 phones numbered 0 1 and 2 at these positions Phone ld X Y depth 0 100 0 5 1 20 200 5 2 150 50 5 Pamguard hydrophone array Array Configuration Static array Towed array Locator Straight rigid Hydrophone v Hydrophone reference point change o x y dmh me 0 100 0 0 0 5 0 Unknown 0 2 20 0 kHz 20 0 200 0 5 0 Unknown 0 2 20 0 kHz 2 150 0 50 0 15 0 Unknown
46. tional detection localisation classification and sound visualisation functionalities The software offers a versatile software hardware interface to enable flexibility in the configuration of in sea equipment number of hydrophones sensitivities spacing and geometry PAMGUARD is a sophisticated software package that can be used by the expert user to set up industry research PAM infrastructure It can also be configured for operational use by MMO PAM operators Central to the software design is a flexible core architecture which allows the integration of a range of additional plug ins For more information on PAM and PAMGUARD please visit www pamguard org This tutorial provides an introduction to PAMGUARD from a user s perspective This involves exercises in setting up and running the software with a variety of configurations of plug in modules The table below shows the core Built in and a selection of the plug in modules some of which will be utilised in this tutorial Core modules are always present in a version of the PAMGUARD application whereas plug In modules are optional and can be added and removed as suits a given monitoring activity ce PAMGUARD V 1 2 00 Tutorial Array configuration MAP Model Manager and Profiler NMEA GPS Acquisition GUI Container for plugins Acquisition devices Help Manager FFT Spectrum factories Configuration and settings manager Decimator Standard graphics layout classes Sound recording Spectrog
47. tithreading can speed up PAMNGUARD execution by utilising all cores on multi processor machines Set Defaults Figure 38 Disable Multi Threading Ex 10 2 Add a Likelihood Detection Module From FileAdd Modules gt Detectors select the Likelihood Detector This will ask you to also add a Sound Acquisition module because it depends on it for data Figure 39 Select OK Module dependencey manager a The Likelihood Detector you are trying to create requires 4 lt i Sound Acquisition before it can operate Do you wish bo go ahead and create a Sound Acquisition Cancel Figure 39 Sound Acquisition Dependency Next you will be asked to provide a name for both the Sound Acquisition module and the likelinood detection module For this exercise simply accept the default names See Figure 40 and Figure 41 38 PAMGUARD V 1 2 00 Tutorial Module Name Mew Module Mame Module name for new Sound Acquisition Sound Acquisition Figure 40 Naming the Sound Acquisition Module Module Name New Module Mame Module name For new Likelihood Detector Likelihood Detector Figure 41 Naming the Likelihood Detector Module Ex10 3 Configure the Sound Acquisition The Sound Acquisition module must now be configured to play back a file From the Detection menu select Sound Acquisition For the Data Source Type choose Audio File then press the Select File button and browse to where you saved the Mo
48. uraged to experiment with PAMGUARD as you work through each one PAMGUARD V 1 2 00 Tutorial Exercise 1 Installing PAMGUARD The PAMGUARD software can be downloaded from the PAMGUARD sourceforge site at https sourceforge net projects pamquard All tutorial exercises can be complete with the latest Core or Beta releases lf you are running under Windows then take one of the exe type installers e g Setup PamguardBeta_1_ 3 00 exe run the executable and launch PAMGUARD from the Start menu lf running on a Mac or under Linux download one of the platform independent jar files e g PamguardBeta_1_3 02 jar Refer to your operating system and Java documentation on how to launch the program Other things you need You will also need to download the sample sound files from the sourceforge site and example configuration files from the psf file download link available at http www pamquard org pamquardTutorial shtml Exercise 2 PAMGUARD familiarisation Ex 2 1 Launching PAMGUARD lf you are running PAMGUARD under Windows then use one of the exe type installers Running the installer will place a shortcut in the Windows Start menu and you should use this to launch PAMGUARD Otherwise on Mac or Linux locate the PAMGUARD ar file on your computer and double click it The following dialogue will appear Load PAMGUARD configuration from x Recent configuration files PaMTutorial1 psf bg Options W Always show at st
49. will now use the Data Model display Select File gt Show data model from the main menu This will open up a new Data Model display window 14 PAMGUARD V 1 2 00 Tutorial o PAMGUARD Data Model one window per PAM module 0 0 NMEA PS GPS Data i Map Comments fO Clicks Click Trigger Function Tracked Clicks Filtered Data fram CO1 CDi Click Trains CD1 Tracked Click localisations Figure 12 The PAMGUARD Data Model window Place your cursor anywhere on an empty space on the data model display area and clicking the right mouse button select Add Modules User Display panel from the drop down menus Enter User Display 1 as the name of your panel in the new module dialogue and click OK Note that the User Display module does not appear as part of the data model This is because the user display cannot receive or produce data and acts merely as a canvas for other displays Click Close at the bottom of the Data Model display window To add the Spectrogram Display to the new User Display panel select the User Display tab on the tab panel selector Notice the main menu items change as you select the various tabs Select User Display gt New Spectrogram from the main menu The spectrogram display requires spectrogram data in order to work so the following dialog will appear Module dependencey manager l x P The Spectrogram you are trying to create requires a FFT Spectrogram Engine before it can opera
50. z for the kernel width Make the vertical scale factor 0 2 Close this dialog box Spectrogram Correlation Parameters x Daka Source Basic FFT S12 pt FFT W Channel 0 Spectrogram Correlation Segment 1 0 _ a Ca Segment 1 ho We Boo Segment 3 ee ee Segment 4 ee Kernel width Hz f M Use log scaled spectrogram Display scaling Vertical scale Factor jo o2 l Peak picking Threshold jis Min time over threshold o 00000 Min time before next detection 0 doong Cancel Figure 20 Parameter settings for the spectrogram correlation example Right click on the spectrogram and choose Settings Select 1 panel and hit enter then go over to the Scales tab There choose a frequency range of 10 50 Hz by setting the min and max frequency and set the amplitude range to 160 190 dB The number of pixels per FFT will depend on the size of your display try 3 to start Next on the Plugins tab make sure the spectrogram correlation graphics checkbox is checked Click Ok 24 PAMGUARD V 1 2 00 Tutorial Now you re ready for Detection gt Start on the menu You should see blue whale calls appear in the spectrogram between about 15 and 20 Hz and a detection function appear below the spectrogram The detectio
Download Pdf Manuals
Related Search