User Manual R2.03 - NEAR Lab
Contents
1. a a 200 Me 500 won f 500 400 Pa on EE 500 200 G 0 500 1000 1500 E 10 Figure 23 Pseudocolored image map representing depth with color and transects overlaid 20 SurfaceTesti Region 1 E fa x File Edit View Insert Tools Desktop Window Help n s k aa nS 2 08 50 Y m 0 200 400 600 800 1000 1200 1400 1600 1800 x im Figure 24 The raw transects colored according to depth Once the surface estimation is complete you may browse to the directory you designated to see the resulting output files Figure 25 There is another Log txt file similar to the one described in section 3 2 Also notice two csv files two per region you selected One is in Latitude Longi tude coordinates and the other is in the Universal Transverse Mercator UTM coordinate system This coordinate system uses a projection that employs sixty zones the corresponding UTM zone is indicated in the file name You can find more information on the UTM coordinate system at http en wikipedia org wiki Universal_Transverse_Mercator_coordinate_system The two csv files may be imported into a package such as ArcGIS and display them in ArcGlobe in their correct locations f surfacerestt A File Edit View Favorites Tools Help Y sx gt Bi j Search gt Folders E x ie BBL Address E Cr EchoMapResultsiHalfMoonTestCsvCutputi Surface Test 1 0 El Los beet BL UTMZonel QRegion1 CSV Figure 25 File output from2. Figure 4 MCRInstaller installation screens 2 2 Editing the System Path Begin by opening the Control Panel window if you are in WindowsXP this can be done by selecting Start gt Settings gt Control Panel Double click on the System option In WinXP you may have to switch to Classic View in order to see this option Figure 5 5 stem Restore z lis Automatic Updates Renate y General L Computer Mame Hardware Advanced System Microsoft Windows sP Professional Version 2002 Service Pack 2 Registered to MCECS Portland State University Ae 4 640 0082461 25815 Computer Intel A Pentium R 4 CPU 3 006 Hz 3 00 GHz 1 39 GB of RAM Physical Address Extension Figure 5 Windows XP Control Panel Next click the Advanced tab and select Environment Variables Figure 6 Highlight the Path variable and select Edit Add a semicolon to the end of the string and add the path to which the MCR library was installed For default is C Program Files MATLAB MATLAB Component Runtime v74 runtime win32 but this must be verified Click OK and reboot the com puter You should now be able to run the MATLAB generated standalone executable The exe cutable can be run in one of two ways 1 double click on the executable file in Windows Explorer or 2 open a DOS command window navigate to the proper directory and type in the executable file name Note that if you use the second option you may be provided with error information that
3. and depth estimation and the asso CAT Output Niles e arieso te ao AAA 5 MCRInstaller installation screens 6 MCRInstaller installation screens T MCRInstaller installation screens 8 Windows XP Control Panel a 9 Environment Variables window a s s 514 244288864 ose ss ee dd 10 An example of EchoMap extracting the compressed library 10 EchoMap startup screen 24 teehee Ge ns whe SEER SER ew BSS 11 The next screen will have a text box that points to the current directory Click on the button to its right to locate the directory of slg files you wish to convert 11 Locating slg files you wish to convert using Windows Explorer 12 alo direcion located s aa veros catarro 12 Type a session name in the box marked sessionName default is current date The session name will be used for the name of the subdirectory inside the root save directory 13 Next select the directory to store the converted files which will be stored in a subdi rectory based on the session name Either type in the name or click the small button next to slgDirectory to get this screen 13 Conversion status Indicator 2 022 258 88 we ee ee we ee 2 2 des 13 Files created after running the conversion operation 14 Echogram subdirectoty s a s ece aw at dtap
4. instructions on setting your system path if this error occurs Install held Wizard Preparing to Install MATLAB Component Runtime Setup is preparing the InstallShield Wizard which will guide you through the program setup process Please wait Extracting MATLAB Component Runtime ms 5 MATLAB Component Runtime InstallShield Wizard MATLAB Component Runtime The MathWorks Welcome to the InstallShield Wizard for MATLAB Component Runtime The InstalShieldie Wizard will install MATLAB Component Runtime on your computer To continue click Next WARNING This program is protected by copyright law and international treaties Copyright 1984 2005 The MathWorks Inc Figure 2 MCRInstaller installation screens ie MATLAB omponent Runtime InstallShield Wizard Figure 3 MCRInstaller installation screens ig MATLAB Component Runtime InstallShield Wizard Installing MATLAB Component Runtime The program features you selected are being installed Please wait while the InstallShield Wizard installs MATLAB Component Runtime This may take several minutes Status Generating script operations For action Installshield i MATLAB Component Runtime InstallShield Wizard MATLAB Component Runtime InstallShield Wizard Completed The InstallShield Wizard has successfully installed MATLAB Component Runtime Click Finish to ext the wizard The Mat Hi Vorks
5. ise A 2 14 Surface estimation screen 15 EchoMap first will cleanup transects e g remove corrupted files and invalid depth DOO e e posar aa AA 15 After transect cleanup you will see the plot displaying the transects on a centered Mercator meter scale os 2 RSS SNS AN ER SRE et SEES SSS 16 The directions on the right explain how to navigate i e zoom in out and select the vertices of rectangles for separate transect regions Shown here is one region selected 17 A three dimensional bathymetry estimate generated by EchoMap 18 Another alternative viewing angle three dimensional bathymetry estimate generated Dr EONO 2 es aka wha oa ee AR nn 19 Pseudocolored image map representing depth with color and transects overlaid 19 The raw transects colored according to depth 20 File output from surtace estimations vs 6844 hb ee de we HEE HO 20 Select the converted chart file e 21 Screen to select the range desired as well as a threshold filtering value 21 Example echopgrani s s 4 664 KS ESE maada ameta rana aa aaea SS 22 Estimates of Half Moon coral reef using four different kernel widths Images were generated in MATLAB 23 1 Introduction 1 1 Author Information This work was performed by a collaboration of the Northwest Electromagnetics and Acoustics Re search and Bio
6. large kernel width depend on the feature size morphology of the actual surface and grid spacing Figure 29 illustrates how varying the kernel width affects the estimate of the surface The data used are from the Half Moon Caye region The small kernel widths of 10m in Figure 29 a and 25m in Figure 29 b effect estimates that are likely much more variable than the actual surface The large kernel width of 200m Figure 29 d over smoothes and thus obscures some of the reef morphology For this case the best kernel width is probably between 40 100 m as illustrated in Figure 29 c which uses a kernel width of 55 m 200 200 E 400 E 400 z z 3 600 3 600 800 800 2000 2000 1000 1000 2000 0 0 x m 0 0 x m ym a ym a Kernel width 10m b Kernel width 25 m 200 200 400 400 z z 2 600 3 600 800 800 2000 2000 1000 1000 2090 0 0 x m 0 0 x m ym o ym c Kernel width 55m d Kernel width 200 m Figure 29 Estimates of Half Moon coral reef using four different kernel widths Images were gener ated in MATLAB 24 4 2 Grid Spacing The size of the grid of estimated depths is based on the minimum and maximum x and y values from the slg files Smaller grid spacing will produce grids of finer positional resolution at the expense of greater computation time For a first run through a data set use a larger grid spacing to speed up processing Once the kernel width is adjusted to th
7. startup screen You will see a screen similar to Figure 17 Here you need to identify the SummaryData mat file you wish to process select a save directory pr aj sessionName SurfaceTestt saveLirectorvCs C EchoMapiResultsiHalfMoonTestiCsvOutput L kernelv idth 50 qridspacing 3 gosUropoutLimit 100 maxGridSize 1000 PlotsD Surface v Plotimagemap PlotkawTransects Select the summary file you wish to process CiEchoMapiResultsiHalMoonTestiSummaryFile m Portland State University The Mature Conservancy Figure 17 Surface estimation screen for the csv files for future use in other software packages such as ArcGIS the kernel smoothing parameters see sections 4 1 and 4 2 and whether you want EchoMap to generate figures After confirming your choices EchoMap will cleanup the data for example remove invalid depths and corrupted files Figure 18 Next you will see plot of the transects Figure 19 Here you may 21 gt Transect cleanup 99 0 00 01 Started at 10 14 51 cou time used 0 00 03 Figure 18 EchoMap first will cleanup transects e g remove corrupted files and invalid depth portions define rectangular regions to select transect data for separate processing This is useful when the transects are located a great distance apart or if you wish to exclude certain portions The directions to the side explain the commands needed to select the regions Figure 20 To select a region cli
8. EchoMap Installation and Operating Instructions RELEASE 2 03 DRAFT gt Portland State UNIVERSITY EchoMap The authors have taken care in the preparation of this document but make no expressed or implied warranty of any kind Errors or omissions may be present and are the fault of the authors themselves and no others To obtain the latest version of this document or to report errors please contact us at nearlab cecs pdx edu Contents 1 Introduction 4 Lal Author Iniormati n es co uan 4 12 R GIONS Re a DR Do hee ees Bo 4 1 3 What does EchoMap do 4 Lol Daa L Onne wa bat eo tie semis dec ca 5 132 DC DAC LE ES NA AO sos a amaia a AAA docs 5 2 Installing EchoMap 5 A lo REI 5 2 2 Editing the System Path gt a s s s oea ar AAA 9 29 File Extensi n seses 464 ots daa ii dadoa bad ee bene Gees adai 9 3 Running EchoMap 10 mak peleton OGT e sc ne ee doses arde 11 3 2 Converting Sle Files 4 LL oaoa edd ee EE wee EER Ge OHSS 11 3 3 Estimating Surface of Converted Files 15 3 4 Converting and Estimate 21 Sao View ECUOSTamsS lt Mn de he ee 21 4 Depth Estimation 23 ack Kernel SPORE ss essri seese bd atia niies ersen TEEN 23 L RAMO DAC ea ereraa 24 List of Figures 1 CON MH OF KH W WO 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 21 28 29 Block diagram of EchoMap parsing processing
9. choMap ctf The file EchoMap ctf con tains a Ct library of functions used by EchoMap exe The first time this file is executed it will extract the compressed library for its use see Figure 7 ioj xl Microsoft Windows AP Version 5 1 2600 LCG Copyright 1985 2001 Microsoft Corp HN SE E cd lotzj Rese Echo E lotsz j Research EchoMapToolbox EchoMap exe Extracting CTF archive This may take a few seconds depending on the size of your application Please wait GIF archive extraction complete Figure 7 An example of EchoMap extracting the compressed library After running MCRInstaller exe place the files EchoMap ctf and EchoMap exe in a directory of your choice this will be the root directory of EchoMap To start EchoMap double click its icon 11 in Windows Explorer or type the following at the command prompt gt gt EchoMap exe 3 1 Selection Screen The initial selection screen for EchoMap appears in Figure ry JO Choose an Action Convert slg Files O Estimate Surface Convert and Estimate View EchoGram Portland State University The Nature Conservancy Figure 8 EchoMap startup screen There are four options to choose 1 Convert 2 Estimate Surface 3 Convert and Estimate 4 View Echogram i e the sonar return These are the main operations that EchoMap performs Each of these is briefly explained in the following sections 3 2 Converting slg Files This
10. ck the mouse to on the top left and the bottom right of the area that you wish to enclose If you would like to zoom in or out to select a region to enclose select z to zoom in and a to zoom back out or c to start over where you began 16 Figure 19 After transect cleanup you will see the plot displaying the transects on a centered Mercator meter scale 17 il ge gt Hi HE j ane Figure 20 The directions on the right explain how to navigate i e zoom in out and select the vertices of rectangles for separate transect regions Shown here is one region selected 18 Next EchoMap will estimate surfaces for each region you selected If you chose to generate images you will see some similar to Figures 21 24 You may save these images in common image formats l SurfaceTest1 Region 1 En l joj xj File Edit view Insert Tools Desktop Window Help y H KRASS 08 ao Figure 21 A three dimensional bathymetry estimate generated by EchoMap 19 SurfaceTesti Region 1 OI xj File Edit View Insert Tools Desktop Window Help M H 8278 08 90 Figure 22 Another alternative viewing angle three dimensional bathymetry estimate generated by EchoMap SurfaceTesti Region 1 E _ B xj Y File Edit View Insert Tools Desktop Window Help Geusan e008 so 1300 E 1400 4 PS 100 1400 300 m ES gd E E 300 a 1000 4 de A eeeemeereereent E 5 O se E
11. could be useful in debugging any problems that occur while running the executable Additional error information should be recorded within the log file LOG TXT located within the same directory as the EchoMap exe file 2 3 File Extensions One of the files within the MATLAB folder in the Program Files directory has a prf extension Note that this is the same extension as an MS Outlook preference file but it is not Executing this file will erase your current MS Outlook preferences Some files within EchoMap directories have a mat file extension This is the same extension as a MS Access Table but they are Matlab Data Files These files should not be loaded with anything other than EchoMap and will not work in MS Access 10 User variables For lotzj Variable Value Path p iprogramsiperMbin p programsitools TEMP Ci Documents and Settings lotzjiLocal 5 TMP Ci Documents and Settingsilotzj Local 5 System variables Variable Value CLASSPATH JC Program Files Javatjrel 6 0_011lib ComSpec COMINNT systems cmd exe DEFAULTUSERP C Documents and Settings Default User DEPLOY DATE 06 10 2005 DEPLOY_PATH Wisis deploy Figure 6 Environment Variables window 3 Running EchoMap The software must be executed from a location folder of which the user has write privileges There are two files needed to run EchoMap EchoMap exe and E
12. csv Data summary csv Log txt Figure 1 Block diagram of EchoMap parsing processing and depth estimation and the associated output files 1 3 1 Data Conversion The Lowrance echosound unit is a high frequency 50 kHz and 200 kHz single beam sonar It stores the returns from the echosoundings along with the x y coordinate data obtained from the integrated GPS system in a binary data format slg EchoMap converts data from the Lowrance unit into a format that is more compact and convenient for post processing 1 3 2 Bathymetry Estimation The typical data recorded from the Lowrance are in the form of irregular tracks or transects These are used to estimate the morphology of the sea floor i e the bathymetry within a rectangular area specified by the user After converting the Lowrance files to obtain the transect data EchoMap cleans up the transect data For example it removes invalid soundings and interpolates the GPS x y position data to match the sampling rate of the echosounder It also can eliminate outlier transects and allow the user to group clusters of transects for separate processing EchoMap performs a method of statistical estimation kernel smoothing see section 4 1 on the processed data to create a grid of depth estimates at evenly spaced x y coordinate values This allows the user to visualize an estimate of the sea floor morphology in areas in between individual transects EchoMap writes this data in a fo
13. e desired level decrease the grid spacing to produce higher resolution output grid
14. hWame Working DatalMatFilesiHalf Moon CayelMatlab Data Filesi11 May2001EchogramsiEchogramCHAaR Enter a starting index 1 Enter a ending index 1934 Filtering threshold 0 Portland State University The Nature Conservancy Figure 27 Screen to select the range desired as well as a threshold filtering value A Figure 1 File Does 12793808 Ping Number 1 216 430 645 859 1074 1288 1503 1717 1932 T 100 200 300 Depth m D 1000 2000 3000 4000 8000 Distance m Figure 28 Example echogram Relative Intensity 22 23 4 Depth Estimation 4 1 Kernel Smoothing EchoMap currently uses a method of two dimensional nonparametric regression called kernel smooth ing to estimate the depth at evenly spaced grid points Kernel smoothing is a form of weighted averaging with an adjustable parameter the kernel width that allows the user to trade accuracy at known data points for overall surface smoothness The user must experiment with the kernel width to find the most suitable result Using a very small kernel width will be similar to nearest neighbor interpolation and likely produce an estimate that is visually too noisy That is the estimated depth will have a much higher variance than actual the physical surface Similarly using a very large kernel width will likely produce a result that is too smooth and miss key variations in the underlying surface The actual definition of a small and
15. l convert Lowrance binary data files slg to a format that is more compact and used for analysis by EchoMap The user may run EchoMap with these files to create visual estimations of the bathymetry export the bathymetry estimations to a Comma Separated Value CSV file format csv and view the sonar returns from individual slg files The CSV format is convenient for further visualization and analysis and is compatible with common software packages including ArcGIS EchoMap can process a single file or many files depending on the user specified parameters section 3 2 The bathymetry estimation process includes pre processing the data to remove invalid portions and lets the user sort them into regions EchoMap then creates a grid of evenly spaced depth estimates based on this data The results are written to a set of files that can be loaded into GIS Geographic Information System software to visualize a three dimensional model of the collected and processed data A block diagram representation of EchoMap is in Figure 1 Without a software tool such as EchoMap the user must create csv files using the Lowrance SonarViewer program manually edit and process the data e g removing invalid depth data save it into GIS readable format and then perform surface interpolation EchoMap now does all of this The user must simply specify which Slg files EchoMap should process adjust optional parameters as desired and execute Depths along transects
16. medical Signal Processing Laboratories at Portland State University Funding was generously provided through a grant from The Nature Conservancy http nearlab ece pdx edu Northwest Electromagnetics and Acoustics Research NEAR Lab http bsp pdx edu Biomedical Signal Processing BSP Lab http www pdx edu Portland State University PSU http www tnc org The Nature Conservancy TNC e Professor Lisa Zurk and Josef Lotz NEAR Lab e Professor James McNames and Timothy Ellis BSP Lab 1 2 Requirements The user will need the following to run EchoMap e A computer running Microsoft Windows e Data files from a Lowrance brand echosounder e g CHART1 slg e The executable software and files described by this manual 1 3 What does EchoMap do The purpose of EchoMap is to convert Lowrance echosound data from its binary data format to one readable by common software analysis packages EchoMap significantly reduces the time and effort needed to translate the echosound data recorded at sea to a format that is appropriate for analysis and visualization A Lowrance brand echosound unit with memory card write capabilities is required Refer to the user manual for the particular echosound model being used for instructions on saving and transferring data files http www lowrance com The echosound unit must be equipped with an integrated GPS unit to run EchoMap EchoMap is a self executable file that runs in Microsoft Windows EchoMap wil
17. option will convert the binary Lowrance s1g files into a format used by EchoMap for viewing echograms and bathymetry estimation After selecting this option you will designate the directory containing the slg files you wish to convert These steps are illustrated in Figures 9 11 Y aoka slgDirectory CiEchoMap Portland State University The Nature Conservancy Figure 9 The next screen will have a text box that points to the current directory Click on the button to its right to locate the directory of slg files you wish to convert 12 Browse rorrolder O OO O O O E Select Directory to Open 5 Saber Test 5 Selguide BE Ci SonarData G HalfMooncz he E 9 KimbeBay 9 subversion LD Synopsys LD System volume Information ma temp gt tempcopy gt Make New Folder Cancel Figure 10 Locating slg files you wish to convert using Windows Explorer A Locate sle Directory slgDirectory CiEchoMapiHalMoonC aye lga Portland State University The Nature Conservancy Figure 11 slg directory located 13 Next you need to designate a directory in which EchoMap will store the converted files You must enter a session name which EchoMap will use to name the root directory of the converted files see Figures 12 13 j riche nat cava Airartary Ni i Tate rm mand A LPL LPF N AY LR CL AU y CU ao D MICA saveDirectory CiEchomMapiResults sessionMame HalffoonTest P
18. ortland State University The Nature Conservancy Figure 12 Type a session name in the box marked sessionName default is current date The session name will be used for the name of the subdirectory inside the root save directory Select Directory to Open C BATCH LD BJPrinter LD Config Msi LD Documents and Settings y E EchoMap 3 gs L localtexm 3 mayura LD Miktex E 1 En pale A P Make New Folder Cancel Figure 13 Next select the directory to store the converted files which will be stored in a subdirectory based on the session name Either type in the name or click the small button next to slgDirectory to get this screen After clicking OK you will see a status bar that indicates the progress of conversion Figure 14 22 Converting CHART132 589 soundings slg 14 of 60 22 0 02 12 Started at 10 09 14 cou time used 0 00 21 Figure 14 Conversion status indicator 14 Once the conversion process is complete you may browse to the designated save directory which will appear similar to Figure 15 The Log txt file contains information about the processing 10 xi File Edit View Favorites Tools Help tex x r DIA _ Search gt Folders iy E Address c EchoMap Results HalfMoonTest E Go CicsvOutput ae C Echograms File Folder E Lis Ext Text Document fi SummaryFile mat MATLAB M4T File Figure 15 Files created after running the conver
19. rmat that is compatible with ArcGIS a software package that offers powerful methods of visualizing such information 2 Installing EchoMap Before running EchoMap for the first time you must install an additional library To do this run the automated installer MCRInstaller exe which is packaged with the EchoMap software or available on the EchoMap web site Again this is only required once on each machine running EchoMap 2 1 MCR Library The source code for EchoMap was written within the MATLAB software environment and com piled to the C language for distribution see http www mathworks com for more information on MATLAB software The distributed code requires the MATLAB Component Runtime MCR which is a stand alone set of shared libraries that enable the execution of MATLAB M files The library can be installed by executing a self extracting file named MCRInstaller exe Execute file MCRInstaller exe by double clicking the icon or call it from the command prompt The installation wizard will walk through several steps see Figures 2 4 for images of the wizard Once this installation is complete reboot the computer and EchoMap can be executed as per the User Manual instructions It has been observed that the system path variables may not be updated properly during the automated library installation If after MCR installation the error mclmcrrt74 dll is not found occurs the system path must be edited See following section for
20. sion operation and records any errors that may have occurred and is useful for debugging purposes If you are encountering errors please attach the Log txt file in an email along with your questions and send to us at nearlab cecs pdx edu The SummaryFile mat contains all the information from the individual slg files necessary for bathymetry estimation with EchoMap When you want to estimate a surface with EchoMap and export it to a format readable by GIS software this is the file you will need to select The subdirectory Echograms seen in Figure 16 contains the individual files for use with the echogram viewer contained within EchoMap If you wish to view the echogram of a particular slg file run EchoMap select View Echogram and select the desired file Ca File Edit View Favorites Tools Help back r DIA search gt Folders ja E Address E C EchoMapiResultsiHalfiMoonTest Echograms J E E Go E EchogramcHARTZ mat MATLAB M4T File fi EchogramCHART3 mat MATLAB MAT File im EchogramCHART4 mat MATLAB M4T File i EchogramCHARTS mat MATLAB MAT File fi EchogramCHART mat MATLAB M4T File E EchogramCHART mat MATLAB MAT File fi EchogramCHARTA mat MATLAB MAT File e CL A AT mL RAST AR RAT Lil Figure 16 Echogram subdirectory 15 3 3 Estimating Surface of Converted Files If you have previously converted some slg files and wish to estimate the associated bathymetry select Estimate Surface at the EchoMap
21. surface estimation 21 3 4 Converting and Estimate This option is simply a combination of the first two steps Convert followed by surface estimation It is a quicker option if the user plans and doing both operations anyways Immediately following data conversion EchoMap will estimate the bathymetry and output the csv files in the designated directory 3 5 View Echograms This option is for viewing sonar returns of converted files Files can be converted as per sections 3 2 and 3 4 As explained in section 3 2 upon data conversion EchoMap will create a subdirectory of files associated with echogram viewing To view an individual echogram select the View Echogram option in the initial selection screen Figure 8 The next screen Figure 26 will ask you to select the converted chart file you wish to view as an echogram Once a file is selected EchoMap will ask the range you wish to view as well as a 1 Y F F LJ re Select the file you wish to plot CiechoMapiResultsiHalfMoonCayelEchogramsiEchogramCHar m Portland State University The Nature Conservancy Figure 26 Select the converted chart file thresholding value Figure 27 Threshold filtering is commonly applied to filter out values less then the threshold to improve the image This value is set to zero by default but may be set as desired The final result is a grey scale echogram Figure 28 This image can be manipulated or saved in various formats A charnt
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