A User's Guide to HAFU (Hydro
Contents
1. 4 Table 2 Summary table produced by the Generate a passage report proced re M 19 CONVENTIONS USED IN THIS MANUAL Words printed in bold upper case fix pitched typeface indicate commands or key names that are typed into the computer exactly as written E g ESC escape key ENTER Theenter key HAFU The command Words printed in upper case proportional typeface indicate data file types These are always one of RAW ECHO FISH SUMMARY INTEGRATION Words printed in upper case fix pitched typeface indicate the names of directories on the hard drive E g RESULTS Words printed in upper case bold faced italics refer to the names of programs E g QTS PKZIP Phrases surrounded by quotations E g refer to specific menu items or data entry prompts Convert HTI RAW files to PBS RAW file Is this information correct Y N vii ABSTRACT Olsen 1995 Software to complement model 240 split beam echosounder user s guide to HAFU Hydro Acoustic File Utilities and QTS Qualark Tools for S Plus Can Tech Rep Fish Aquat Sci 2037 45p Hydroacoustic Technology Inc s HTI model 240 split beam echosounder represents the state of the art in split beam hydroacoustic technology The split beam technique provides several advantages over traditional echosounder design including the ability to accurately estimate target strengt2. A Overview B QTS User s Manual B 1 The Main Menu eeececocosesccsttossocscosctccseseceseosteoseseveoveceseesceccceceocecccocen ELEC EEE EEE EEE EL EEE Coe ET EEE EEE Perce ESC ES POCO eme B 1 1 View On Line Help B 1 2 Data Dm B 1 3 TMA Bes B 1 4 Histograms B 1 5 Echograms and Trackers NS DECENT B 2 The Data Manipulation Menu B 2 1 Launch HAFU eere B 2 2 Scan a Data File B 2 3 Remove Noise from a Data Frame evecceeccescceseocceoscesseosos secoseoocvocvon ePsesosecocvsoos rreererrre ry seosocssocosoes eeososoooovevs evecececvsoecse ses
3. Scientific Excellence Resource Protection amp Conservation Benefits for Canadians Excellence scientifique Protection et conservation des ressources B n fices aux Canadiens Software to Complement HTI s Model 240 Split Beam Echosounder A User s Guide to HAFU Hydro Acoustic File Utilities and QTS Qualark Tools for S Plus Norm Olsen Biological Sciences Branch Department of Fisheries and Oceans Pacific Biological Station Nanaimo British Columbia V9R 5K6 January 1995 Canadian Technical Report of Fisheries and Aquatic Sciences No 2037 Fisheries P ches 1 1 a and Oceans et Oceans Canada crc CU gt gt gt ee L aM Canadian Technical Report of Fisheries and Aquatic Sciences Technical reports contain scientific and technical information that contributes to existing knowledge but which is not normally appropriate for primary literature Technical reports are directed primarily toward a worldwide audience and have an international distribution No restriction is placed on subject matter and the series reflects the broad interests and policies of the Department of Fisheries and Oceans namely fisheries and aquatic sciences Technical reports may be cited as full publications The correct citation appears above the abstract of each report Each report is abstracted in Aquatic Sciences and Fisheries Abstracts and indexe
4. Backward to move to the previous echogram segment or Pause to rerun the current echogram segment Example ck ce ok oe oe oe oe e oe oe oe che kk kk kk kk kok kk kok ok kok kok EXAMINE TRACKS SELECTED FROM AN ECHOGRAM 3 ck ce ce ce oce eee ce eode ce ce k k oe XX coke oe ok oe ck oce kk ceo ke kk ke Enter RAW data object default is last scanned a244 raw Enter ECHO data object default is last scanned a244 ech Enter start day optional 244 Enter start hour optional 2 Enter start minute optional 30 Enter start range in meters optional 2 Enter end range in meters optional 10 Enter beam x section width optional default 10 degrees off axis 10 Fig 28 Screen display of the Echogram examiner routine 33 5 3 Target track examiner This item produces a set of six plots that allow you to compare a tracked target with surrounding echoes Fig 29 The top left plot shows the tracked target in the beam cross section X vs Y in meters The plot to the right of this shows the tracked target with respect to horizontal position and range X vs Z in meters The top right plot shows the ping sequence represented by the tracked target the ping number of each echo returned from the target relative to the total number of pings since the start of data collection vs the horizontal coordinate in meters The circles s
5. This item produces a standard on screen echogram that can be paged through in 6 minute intervals Fig 27 Echoes are displayed as short black vertical bars Grid lines divide the x axis into 1 minute intervals and the y axis into 1 metre intervals Example coco ceo x x x n xA x ECHOGRAM kkekkkkkkk kkk Enter data object to plot default is last RAW scanned a255 raw Enter start day optional 255 Enter start hour optional 2 Enter start minute optional 0 Enter start range in meters optional 2 Enter end range in meters optional 9 Enter title for plot enter for none Echogram for Day 255 18 3 Tims hh mm Fig 27 Echogram as produced by the Simple echogram menu item 32 B 5 2 Echogram Examiner This item produces an echogram of a RAW and an ECHO data frame Fig 28 Echoes are shown as short vertical bars with untracked echoes from the RAW data frame displayed in black and tracked echoes from the ECHO data frame displayed in some other colour To view the trajectories of individual tracked targets use the left mouse button to click on each highlighted track with the mouse pointer When you have selected all the tracks you wish to view click the right mouse button You can then view the trajectories of each tracked target on a horizontal vs vertical angle display When you have finished viewing tracks select Forward to move on to the next echogram segment
6. plot a RAW ECHO or FISH data frame Note that when using a FISH data frame all coordinates are defined as the initial position that each fish was detected in the beam B 1 4 Histograms This item brings up the sub menu called Histograms which allows you to choose from several different histogram plots Histograms graphically display the freqency of observation of some variable summed over regular intervals The freqeuncy at each interval is represented by a bar of variable height where the interval with the greatest frequency is represented by the tallest bar Unless otherwise indicated a RAW ECHO or FISH data frame may be plotted 8 B 1 5 Echograms and trackers This item brings up the sub menu called Echograms and Trackers which allows you to choose from echograms and tracker plots Echograms are plots of detected echoes shown on a time horizontal axis vs range vertical axis display Trackers display the trajectory of individual tracked targets B 1 6 Quit This item quits and ends your S Plus session B 2 The Data Manipulation Menu B 2 1 Launch HAFU This item launches HAFU Enter the name of the directory that you wish to run HAFU from This should be the name of the directory containing the HTI files you wish to analyze Note that HAFU can also be run as a stand alone DOS program by entering HAFU at the DOS prompt B 2 2 Scan a data file This item allows you to convert a data file produc
7. SEP 13 1995 Biological Sciences Branch Department of Fisheries and Oceans Pacific Biological Station Nanaimo British Columbia V9R 5K6 Re ional Library E c Minister of Supply and Services Canada 1995 Cat No Fs 97 6 2037E ISSN 0706 6457 Correct citation for this publication Olsen N 1995 Software to complement HTI s model 240 split beam echosounder A user s guide to HAFU hydro acoustic file utilities and QTS Qualark tools for S Plus Can Tech Rep Fish Aquat Sci 2037 45p TABLE of CONTENTS LIST OP FIGURES detente LIST OE TABLES nf nement ne ABSTRACT oor a ete FEE UR aa UT INTRODUCTION Chapter 1 HAFU THE HYDRO ACOUSTIC FILE UTILITIES A Overview B HAFU User s Manual B 1 Screen Elements B 1 1 The Main Menu B 1 2 The Input Window eee 1 3 The Status Window 1 4 The Help Window B 1 5 The Read Window B 2 Menu Items B 2 1 Compress Daily Files B 2 2 Convert HTI RAW files to PBS RAW file Chapter 2 iii B 2 3 Convert HTI ECHO files to PBS ECHO file B 2 4 Convert PBS ECHO file to PBS FISH file B 2 5 Merge RAW files B 2 6 Display Upstream Tracked Fish Counts B 2 7 View Results uiscera tores 2 8 Shell to DOS encens B 2 9 QUIL i gione Ihr nn a ceases TS Qualark Tools for S Plus
8. Upstream m gt Downstream Z Distance from tranzducer m Ping Number Fig 29 Plots produced by the Target track examiner routine 34 APPENDIX A DATA FILE TYPES AND FORMATS The following section describes the format of each type of HTI and PBS data file 1 HTI RAW FILES RAW files include all detected echoes that pass a point source target selection criteria This can include echoes from fish rocks or other point source targets An example RAW file is shown in Fig 1 Start Processing at Port 1 C SB SBPORT1 PAR Wed Oct 12 00 00 02 1994 Data processing parameters used in collecting this file for Port 1 100 1l 1 101 1 0 610 1 611 1 D 94SYS2 B Data processing parameters used in collecting this file for Port 2 100 1 2 101 1 0 610 1 OFF 611 1 D 94SYS2 B Ping Range Sum Chan 6dB 12dB 18dB Up Dn Lf Rt Mux Number meters Volts P W Angle Angle Port 563 3 16 0 5359 10 10 12 2 1950 3 3843 1 564 3 16 0 3034 7 8 8 2 7752 3 2484 1 End Sample Block for Port 1 C SB SBPORT1 PAR Wed Oct 12 00 02 00 1994 264 7 38 0 2173 8 8 8 3 9969 5 6333 2 265 3 91 0 2454 8 8 8 6 4172 2 1934 2 End Sample Block for Port 2 C SB SBPORT2 PAR Wed Oct 12 01 00 00 1994 Stop Processing C SB SBPORT1 PAR Wed Oct 12 01 00 00 1994 Fig 1 Example HTI RAW data file A Section listing the file creation time and date the port on which data collection begins and the parameter values used
9. as those in the PBS RAW file with one additional column fish which is the sequence number of fish since the start of the requested period of data In other words no matter what period of time the user chooses the first fish detected in that time frame is numbered as 1 5 HTI FISH FILES FISH files contain summary information on each target tracked by the system An example FISH file is shown in Fig 6 Start Processing at Port 1 C SB SBPORT1 PAR Wed Oct 12 00 00 03 1994 Data processing parameters used in collecting this file for Port 1 100 1 1 101 1 0 610 1 OFF 611 1 D 94SYS2 B Data processing parameters used in collecting this file for Port 2 100 1 101 1 0 610 1 OFF 611 1 D 94SYS2 B Fish Start End Num Start Start Range Dist Dist Dist Swim Target Mx Num Ping Ping Ech Xcoord Ycoord meters X Dir Dir 7 Dir Speed Streng Pt 352 563 576 7 0 19 0 12 3 16 0 37 0 00 0 34 0 47 30 51 353 890 911 17 0 39 0 23 4 90 0 46 0 02 0 25 1 14 28 42 End Sample Block for Port 1 C SB SBPORT1 PAR Wed Oct 12 00 02 00 1994 354 264 286 14 0 72 0 51 7 38 1 27 0 29 0 08 1 35 30 37 355 985 1001 10 0 33 0 36 4 18 0 51 0 17 0 02 0 95 27 10 End Sample Block for Port 2 C SB SBPORT2 PAR Wed Oct 12 01 00 00 1994 Stop Processing C SB SBPORT1 PAR Wed Oct 12 01 00 00 1994 Fig 6 Example HTI FISH data file Section listing the file creation time and date the port on which data collection begins and the parameter values
10. cancel continue entering information until you are prompted with the Is the above correct Y N prompt then type N followed by ESC eInput ESC to 1 Enter system 1 2 1 Enter year format nnnn 1994 Enter start julian day format nnn Fig 6 The input window of HAFU Information is entered line by line In response to the prompts displayed B 1 3 The Status Window The status window is designed to keep you informed of a specific task s progress since certain tasks can take several minutes to complete This window is also helpful for locating when and where a task fails if an error is encountered Fig 7 shows the status window displaying a task in progress Status Finished decompressing CR CUT NC wait Done A2380000 RAW gt A2380000 SPR B2380000 SPR Done A2380100 RAW gt A2380100 SPR B2380100 SPR Fig 7 The status window of HAFU The progress of the task being performed is displayed in this window B 1 4 The Help Window The help window displays a brief description of each menu item To view help on a particular menu item position the menu pointer next to the menu item and press the F1 key Fig 8 shows the help window displaying help on the Quit menu item To view a more detailed help file press F10 while in the main menu Press ESC to clear HAFU and returns you to the operating system Hel Qui ts Fig 8 The help window of HAFU A brief descri
11. large volumes of data and often does not meet our requirements for detailed data analysis Thus we have developed our own software tools These are grouped under two main categories utilities to concatenate and convert HTI data files into a more useful format and routines to analyze and graphically display the data The first category of software is accessible from the DOS program HAFU which is a menu driven front end for several command line utilities A screen display of HAFU is shown in Fig 3 AFU Hydro acoustic file utilities Conpress Daily Files gt Convert HTI Raw Files to PBS Raw Files Convert HTI Echo Files to PBS Echo Files Convert PBS Echo File to PBS Fish File Merge HTI Files Display Upstream Tracked Fish Counts View Results Shell to DOS Quit 1 Move ENTER Select F1 Help F1 README Fig 3 Example on screen display of HAFU Hydro Acoustic File Utilities The function of each HAFU menu item is outlined in Table 1 aa Table 1 The function of each menu item in HAFU Command arguments are shown in brackets Menu Item User Input Output Command Line Equivalent Compress Daily Year and day of PKZIP format compressed pkzip lt zipfile gt Files the year file containing all data files for datafiles ear and day Convert Raw Year days ofthe PBS format raw file containing rawfiltr lt HTIrawfile gt Files to PBS Raw and start and all Raw file data for muxloutp
12. not generated from HTI FISH files Instead they are a conversion of PBS ECHO files This is done because it is much quicker to convert a PBS ECHO file to a FISH file than it is to convert and concatenate HTI FISH files An example PBS FISH file is shown in Fig 7 40 jd fish startp stime etime 016194 0 016556 890 025278 0 025861 040667 0 041278 060694 0 061139 disty distz 0 0000 0 3403 0 0700 0 1842 0 2900 0 1093 0 1400 0 0122 bpf ts 5 7482 30 5114 10 1784 28 4194 18 3223 30 3729 16 8153 27 1000 Fig 7 Example PBS FISH data file The contents of the PBS FISH file are listed in Table 5 41 Table 5 Contents of the PBS FISH file Column Contents jd e Julian Day defined here as the number of days since January 1st fish e Sequence number of the tracked target Always starts at 1 for any given file startp e Sequential ping number on which the tracked target was first detected endp e Sequential ping number on which the tracked target was last detected stime e Time in decimal hours that the tracked target was first detected A 24 hour clock starting at midnight is used etime e Time in decimal hours that the tracked target was last detected A 24 hour clock starting at midnight is used nump e Total number of pings detected from the tracked target x e Initial horizontal position of the tracked target in meters to the left or right of the vertical axis y e Initial
13. used to collect data on port 1 B Section listing parameter values used to collect data on port 2 C Section listing data collected and times when port switching occurred 39 The contents of the HTI FISH file are listed in Table 4 Table 4 Contents of the HTI FISH data file Fish Num Start Ping End Ping Num Ech Start Xcoord Start Ycoord Range meters Contents Sequential fish number of the tracked target since echosounder began collecting data Sequential ping number on which the tracked target was first seen Sequential ping number on which the tracked target was last seen Total number of echoes detected from the current tracked target Initial horizontal position of the current tracked target in meters to the left or right of the vertical axis Initial vertical position of the current tracked target in meters above or below the horizontal axis Range in meters of the current tracked target s initial position Dist X Dir e Total horizontal distance traveled by the current tracked target in meters Dist Y Dir e Total vertical distance traveled by the current tracked target in meters Dist Z Dir e Total range traveled by the current tracked target in meters Swim Speed e Mean swim speed of the tracked target in meters per second Target Streng e Mean swim speed of the tracked target in dB Mx Pt e Multiplexer port on which the target was tracked 6 PBS FISH FILES PBS FISH files are
14. user s manual for a set of software tools designed to complement HTI s model 240 split beam digital echo sounding system Two packages are covered in this manual a DOS based set of file management utilities called HAFU Hydro Acoustic File Utilities and a Windows based set of S Plus routines called QTS Qualark Tools for S Plus Both sets of software are accessible from a menu system that runs from within S Plus for Windows and additionally HAFU can be accessed as a stand alone DOS program HTPS SPLIT BEAM ECHOSOUNDING SYSTEM HTT s Model 240 200 KHz Split Beam Hydroacoustic System consists of a split beam echosounder a monitor and keyboard two transducers an oscilloscope a chart recorder a digital audio tape recorder a 486DX personal computer and a 24 pin dot matrix computer printer Fig 1 Model 240 Spllit Beam Monitor P a Echosoun under ecmcncope Computer Printer Ean macs AR Chart Recorder Chart Recorder Mode Printer Digital Audio Tape Recorder Real Time Graphical Display Tape Recorder Model 464 Digital Multiplexer Real Time Analysis Computer Model 340 Split Beam Digital Echo Processor Fig 1 Schematic diagram of HTI s model 240 split beam hydroacoustic system as configured at Qualark From HTI 1993 Rotator Control Split Beam Transducers Unlike conventional echosounders that can only determine the range of a target a split beam echosounder can measure the th
15. vertical position of the tracked target in meters above or below the horizontal axis 2 e Initial 2 coordinate range projected onto the beam axis of the tracked target in meters from the face of the transducer range e Initial range of the tracked target in meters from the face of the transducer distx e Total horizontal distance traveled by the tracked target in meters disty e Total vertical distance traveled by the tracked target in meters distz e Total z distance range projected onto the beam axis traveled by the tracked target in meters speed e Mean speed of the tracked target in meters per second vert e Initial vertical position of the tracked target in degrees above or below the horizontal axis horiz e Initial horizontal position of the tracked target in degrees to the left or right of the vertical axis phi e Initial spherical coordinate of target see Fig 3 theta e Initial spherical coordinate of target see Fig 3 SCV e Peak output voltage summed over all 4 quadrants of the transducer bpf e Beam pattern factor ts e Mean target strength of the tracked target in dB Neither HAFU nor QTS use the HTI SUMMARY or HTI INTEGRATION files so they are not covered here Refer to HTI documentation for details on these file types 42 APPENDIX B FILE NAMING CONVENTIONS HAFU was originally designed to deal with the specific configuration that we use at our site at Qualark Creek on the Fraser River Thus t
16. 1 Main Menu Items B 1 1 View on line help This item accesses a Windows help file on QTS The help system includes standard Windows help features such as hypertext links that allow you to to jump to topics by clicking on certain words or phrases indicated by green underlined text See the Windows user manual for more information on using this help system Fig 16 shows the Windows help system running the QTS help file ualark Tools for S Plus Qualark Tools for S Plus Contents Scanning in a data file interactively removing noise from data Images Histograms Echograms and Trackers Fig 16 The 075 help system B 1 2 Data manipulation This item brings up the sub menu called Data Manipulation which provides items to convert data files to S Plus format to edit data sets interactively and to create summaries of fish passage B 1 3 Images This item brings up the sub menu called Images which allows you to choose from several different image plots Images are two dimensional histograms in which two variables form a grid of some pre defined spacing The number of observations falling within each cell of the grid is summed and the relative difference in frequencies among cells is indicated by differences in cell colour or shades of gray For gray scale images cells with no observations are coloured black while the the cells with the highest number of observations are coloured white For all of these routines you may
17. 5 7504 26 3579 3 2484 4 2686 139 5000 0 3034 6 4053 30 6444 2 3359 3 8181 127 6786 0 3650 5 1088 30 3354 2 6008 6 7508 292 5654 0 2130 18 0709 22 0515 Fig 2 Example PBS RAW file split The contents of the PBS RAW file are listed in Table 2 36 Table 2 Contents of the PBS RAW file Column Heading Contents jd e Julian Day defined here as the number of days since January Ist time e Time in decimal hours on which ping occurred A 24 hour clock starting at midnight 0 00 is used ping e Sequence number of ping as recorded in the HTI RAW file X e X position of target in meters to the left or right of the vertical axis y e Y position of target in meters above or below the horizontal axis 2 e Z position of target range projected onto beam axis in meters from the face of the transducer range e Range of target in meters from the face of the transducer pw e Pulse width at 12dB from peak voltage vert e Vertical position of target in degrees above or below the horizontal axis horiz e Horizontal position of target in degrees to the left or right of the vertical axis phi e Spherical coordinate of target Fig 3 theta e Spherical coordinate of target Fig 3 SCV e Peak output voltage summed over all 4 quadrants of the transducer bpf e Beam pattern factor ts e Target strength in dB Fig 3 Illustration of spherical coordinates phi and theta 0 See Peterson 1960 for a complete des
18. 94 1994 After concatenation with the HTI RAW files procedure of HAFU 2435 APPENDIX C INPUT CONVENTIONS USED IN HAFU When entering data into HAFU s input window the following conventions are always used e System number is entered as a 1 or a 2 corresponding to the first or second echosounding system respectively This is an historical consequence of our use of two systems at Qualark e The year is entered as a 4 digit number for example 1995 The day is entered as a 3 digit number beginning at 001 on January 1st of each year and ending at 365 on non leap years and 366 on leap years We use the term Julian Day to describe this number although this is not a technically correct definition of Julian Day e The time is entered as a 4 digit number representing hours and minutes beginning at 0000 at midnight and ending at 2400 APPENDIX D MISCELLANEOUS HAFU UTILITIES Two useful utilities can be found in the HAFU program directory These are designed to be run from the DOS command line and convert a given Julian Day to a calendar date and vice versa The program to convert a Julian Day to a calendar date is called JD2DATE and the program to convert a calendar date to Julian Day is called DATE2JD They are used as follows JD2DATE julian day year Where julian day the Julian Day year the year e g gt jd2date 201 1995 Julian Day 201 1995 July 20 1995 DATEAJD
19. Distance From Transducer Fig 20 Z vs X density image 25 B 3 3 X vs Y This item produces a density image of target frequency in the X horizontal coordinate in meters vs Y vertical coordinate in meters plane Fig 21 A scatter plot of the same data set is shown to the right of the image Example cfe coke ode eee k k k k k e e de che de ke eoe de ode oe eee e e IMAGE OF X HORIZONTAL VS Y VERTICAL de e k fe de de k k oe de ke ke oe de dede je eoe de ee ecce je dee de ke oe e je ke e de de ode ve Enter data frame to plot default is current ECHO a244 ech Enter title for plot Echo Data Target Density by Up Down Lelt Right Angle Day 255 Tracked Echoes Density Image Scatter Plot Left Right Angle Left Right Angle Fig 21 X vs Y density image 26 B 3 4 TS vs off axis angle This item produces a density image of target strength in decibels vs off axis angle angle from the centre of the beam in degrees Fig 22 A scatter plot of the same data set is shown below the image Note that this plot is only appropriate for beams with circular cross sections Example Woke kkk ek kok ek kok ek ke ok kok kok kok ke ke ok kok ok kok ok kek kok ake kok ok ok IMAGE OF TARGET STRENGTH VS OFF AXIS ANGLE kakk kaka ka kkk kkk kk kkk kkk kkk kk kkk kkk kkk Enter data frame to plot default is current ECHO a244 ech Enter title for plot Echo Data Target Streng
20. ILE TYPES AND FORMATS 1 HTI RAW files AJ2 PBS RAW Iles aste been A3 HITECHO files Ad PBS ECHO AO HTI FISH files oiii eot o reae eleme BRE A 6 PBS FISH files Appendix B FILE NAMING CONVENTIONS Appendix C INPUT CONVENTIONS USED IN Appendix D MISCELANEOUS HAFU UTILITIES REFERENCES rennes Cr 20 21 21 22 22 23 23 24 25 26 27 27 28 29 30 31 31 32 33 34 34 35 37 38 38 39 42 43 43 45 Fig 1 Fig 2 Fig 3 Fig 4 Fig 5 Fig 6 Fig 7 Fig 8 Fig 9 Fig 10 Fig 11 Fig 12 Fig 13 Fig 14 Fig 15 Fig 16 Fig 17 Fig 18 Fig 19 Fig 20 Fig 21 Fig 22 Fig 23 Fig 24 Fig 25 Fig 26 Fig 27 Fig 28 Fig 29 LIST of FIGURES Schematic diagram of HTI s model 240 split beam hydroacoustic system as configured at Qualark sees Example on screen display of HTT s DSBP software Example on screen display of HAFU the Hydro Acoustic QAM Flow diagram of HAFU s operation The main menu of HAFU csetera te e Eee rapa blague The input window of HAFU eese The status window of HAFU esee The help wind
21. When you have finished viewing files continue to press ESC until you are back at the HAFU main menu A2380000 ALR B2380000 ALR Fig 11 The nEsuLTS directory with two PBS RAW files listed One represents data collected on port 1 A2380000 ALR the other represents data collected on port 2 B2380000 ALR B 2 3 Convert HTI ECHO files to PBS ECHO file This item operates identically to the Convert HTI RAW files to PBS RAW file item except that the resulting files are ECHO format not RAW Follow the steps outlined in B 2 2 to use this procedure 12 B 2 4 Convert PBS ECHO file to PBS FISH file This item converts PBS ECHO files created with the item Convert HTI ECHO files to PBS ECHO file to PBS FISH files To use this item enter the name of the PBS ECHO file you wish to convert and the ping rate used to collect the data You are asked to verify your entries before the conversion takes place During the conversion the status window displays the prompt Processing and when completed the source PBS ECHO file and target PBS FISH file names are displayed Fig 12 When the conversion is complete press any key to return to the HAFU main menu Processing Done a2380000 ale gt a2380000 a1f at 10 pings sec Conversion complete Press a key to continue Fig 12 Status window upon completion of PBS ECHO file to PBS FISH file conversion B 2 5 Merge HTI RAW files Occasionally it s necessary to rep
22. ce if the user wishes to look at the raw data for a particular time frame she needs to enter only the dates and times desired and the relevant files will be decompressed from the compressed file converted to PBS format and concatenated into a single flat file that can be read into a spreadsheet or other analysis software Any intermediate stages between the compressed file and the PBS format file are deleted during the process Fig 4 schematizes the operation of HAFU Refer to appendix A for a complete description of HTI and PBS file types and their formats HTI farmat data RAW ECHO FISH SUMMARY INTEGRATION L HAFU 5i rs Hydro Acoustic File Utilities 5 PKZIP compressed file ECHO FISH HTI format RAW files PBS format data files Fig 4 Flow diagram of HAFU s operation B HAFU USER S MANUAL To begin a HAFU session change to the directory containing the HTI data files you wish to analyze and enter HAFU at the DOS prompt The program begins by creating two sub directories under the current directory one called RESULTS and one called V TEMP if they do not already exist The RESULTS directory stores PBS format files resulting from any of HAFU s conversions of HTI files The V TEMP directory is temporary storage location for any HTI files that are extracted from a compressed file and for intermediate files between HTI and PBS formats You may delete the directory after your HAFU session is
23. completed If you wish to delete the N RESULTS directory first move the files you want to keep into an alternate directory B 1 Screen Elements B 1 1 The Main Menu The first menu displayed when HAFU starts is shown in Fig 5 To select a menu item use the up and down cursor control keys 1 5 to position the menu pointer gt next to the menu item of your choice and press ENTER Compress Daily Files Convert HTI RAW Files to PBS RAW File Convert HTI ECHO Files to PBS ECHO File Convert PBS ECHO File to PBS FISH File Merge HTI RAW Files Display Upstream Tracked Fish Counts View Results Shell to DOS Quit ENTER Select F1 Help F10 README Fig 5 The main menu of HAFU The menu pointer is initiaily positioned next to the first item Daily Files B 1 2 The Input Window Most of the menu items require that you enter certain information usually the days and times of the period you wish to extract data for This information is entered into the input window shown in Fig 6 The input window appears just below the main menu after you select a menu item that requires input If you wish to cancel the menu item that initiated the input window you must hit the ESC key first before responding to any of the input prompts This will return you to the main menu Once you begin to enter your choices hitting the ESC key will not cause the item to cancel If you begin entering information and then later wish to
24. cription of the spherical coordinate system ranges from 0 to T while ranges from 010 27 2g s 3 HTI ECHO FILES ECHO files contain information on each ping returned from targets that are tracked An example ECHO file is shown in Fig 4 Start Processing at Port 1 C SB SBPORT1 PAR Wed Oct 12 00 00 02 1994 Data processing parameters used in collecting this file for Port 1 100 1 1 101 1 0 610 1 OFF 611 1 D 94SYS2 B Data processing parameters used in collecting this file for Port 2 100 1 2 101 1 0 610 1 OFF 611 1 D 94SYS2 B Fish Ping X dir Y Dir Range 6 12 18 Sum Ch Beam P Target Num Coord Coord meters PW Volts Factor Strength 563 0 19 0 12 3 16 10 10 12 0 5359 5 7482 26 36 564 0 18 0 15 3 16 7 8 8 0 3034 6 4021 30 65 End Sample Block for Port 1 C SB SBPORT1 PAR Wed Oct 12 00 02 00 1994 354 264 0 72 0 51 7 38 8 8 8 0 2173 18 3223 21 63 354 268 0 52 0 29 7 38 8 8 8 0 2960 7 8267 29 44 End Sample Block for Port 2 C SB SBPORT2 PAR Wed Oct 12 01 00 00 1994 Stop Processing C SB SBPORT1 PAR Wed Oct 12 01 00 00 1994 Fig 4 Example HTI ECHO data file A Section listing the file creation time and date the port on which data collection begins and the parameter values used to collect data on port 1 B Section tisting parameter values used to collect data on port 2 C Section listing data collected and times when port switching occurred The contents of th
25. d in the Department s annual index to scientific and technical publications Numbers 1 456 in this series were issued as Technical Reports of the Fisheries Research Board of Canada Numbers 457 714 were issued as Department of the Environment Fisheries and Marine Service Research and Development Directorate Technical Reports Numbers 715 924 were issued as Department of Fisheries and the Environment Fisheries and Marine Service Technical Reports The current series name was changed with report number 925 Technical reports are produced regionally but are numbered nationally Requests for individual reports will be filled by the issuing establishment listed on the front cover and title page Out of stock reports will be supplied for a fee by commercial agents Rapport technique canadien des sciences halieutiques et aquatiques Les rapports techniques contiennent des renseignements scientifiques et techni ques qui constituent une contribution aux connaissances actuelles mais qui ne sont pas normalement appropri s pour la publication dans un journal scientifique Les rapports techniques sont destin s essentiellement un public international et ils sont distribu s cet chelon Il n y a aucune restriction quant au sujet de fait la s rie refl te la vaste gamme des int r ts et des politiques du minist re des P ches et des Oc ans c est dire les sciences halieutiques et aquatiques Les rapports techniques peuvent tre cit s comm
26. defined as eft to right or right to left as seen from the river bank looking out into the river Example 3e ce eoe ce oe oe oe oe oe eoe oe e ok e e e kx GENERATE DAILY REPORT oce ce koe e e ce e ede dede e de eode Enter source FISH data frame default is last FISH file scanned a255 fsh Enter number of minutes of data collected per hour default is 60 min 30 Enter the direction of water flow right to left or left to right Default is left to right left to right Enter title Table 2 Summary table produced by the Generate a passage report procedure Unvalidated Expanded Fish Passage Julian Day s 244 to 244 Flow Left to right Expansion Factor 2 Julian Start End Up Down Avg Avg Day Hour Hour Stream Stream TS Speed 244 0 1 228 28 29 58 1 23 244 1 2 278 60 28 59 1 45 244 2 3 218 56 28 75 1 39 244 3 4 260 58 28 6 1 39 244 4 5 356 140 28 23 1 48 244 5 6 120 14 27 33 1 45 244 6 7 102 14 27 55 1 42 Total Passage 1562 370 Hourly Mean Passage 223 14 52 86 28 38 1 4 Multiplexing refers to switching echousounder operation between two transducers at some regular interval 21 Unvalidated Expanded Fish Passage Julian Day s 244 to 244 Flow Left to right Expansion Factor 2 A R 8 8 a B SS 0 1 a 3 4 5 Hour Downstream passing tich are chown below axis Fig 18 Plot produced by the Generate a passage report menu
27. density image of target frequency in the Z Distance from the transducer face in meters vs Y vertical coordinate in meters plane Fig 19 A scatter plot of the same data is shown below the image Example 3e he e dee che ee dee ee ede dee oe he de dee dede de ode hee eode hehe e dee e IMAGE OF Z RANGE VS Y VERTICAL kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk Enter data frame to plot default is current ECHO a244 ech Enter title for plot Echo Data Target Distribution in Z Y Pane Day 255 Tracked Echoes Density image Y vertical Pos Distance From Tanzducer Scatter Plot Y vertical Portion Distance From Transducer Fig 19 Z vs Y density image 24 B 3 2 Z vs X This item produces a density image of target frequency in the Z Distance from the transducer face in meters vs X horizontal coordinate in meters plane Fig 20 A scatter plot of the same data set 1 shown below the image Example IMAGE Z RANGE VS X HORIZONTAL koe oe 0e oe oec oko oe ce oe ke oec e 0e oe ce ce ke eoe oe KO Ke e x Enter data frame to plot default is current ECHO a244 ech Enter title for plot Echo Data Target Distribution inZ X Plane Day 55 Tracked Echoes Density Image X Horizontal Pos 6 Distance From Tanzducer Scatter Plot X Poe thon 5
28. e verification screen Once you press Y HAFU searches the current directory for a compressed file that matches the input criteria If the appropriate compressed file is found any See appendix C for a complete description of input conventions See appendix B for a complete description of naming conventions 11 RAW files that fall within the period specified are extracted and converted to PBS format HAFU uses information found in each file s parameter section to calculate additional variables of interest such as beam pattern factor and target strength The parameter sections are then left out of the resulting PBS RAW files When all conversions are complete the PBS RAW files are concatenated together into two files containing the information for the specified period of interest One file contains data collected on port 1 and the other contains data collected on port 2 Note that if only one port was used to collect data the file representing data from the other port consists of only a single header line This file should later be deleted When the conversion process is complete the display switches to a view of the RESULTS directory showing a list of the files contained there Fig 11 This list includes the PBS RAW files that were just produced as well as any PBS files from previous procedures To view any of these files use the cursor control keys 0 0 to position the highlight bar over the file name and then press ENTER
29. e HTI ECHO file are listed in Table 3 Table 3 Contents of the HTI ECHO data file __ Column Headin Contents Fish Num e Sequential fish number since echosounder began collecting data Ping Num e Sequential ping number since the file start time X Dir Coord e Horizontal position of target to the left or right of the vertical axis in meters Y Dir Coord e Vertical position of target above or below the horizontal axis in meters Range meters e Range oftarget in meters from the face of the transducer 6dB PW e Pulse width received at 6dB from peak voltage 12dB PW e Pulse width received at 12dB from peak voltage 18dB PW e Pulse width received at 18dB from peak voltage Sum Ch Volts e Peak output voltage summed over all 4 quadrants of the transducer Beam P Factor e Beam pattern factor Target Strength e Acoustic size of target in dB 38 4 PBS ECHO FILES As is the case with RAW files HAFU uses information contained in the parameter section of the HTI ECHO file to calculate additional fields after which the parameters are discarded An example of a PBS ECHO file is shown in Fig 5 jd time fish ping pw 285 0 016194 1 563 000208 285 0 016222 564 000146 1 0 016250 1 565 000167 0 016333 1 568 000229 phi theta 0780 147 7244 2523 140 1944 8504 129 0939 4753 112 6199 Fig 5 Example PBS ECHO file split The column headings of the PBS ECHO file are the same
30. e des publications compl tes Le titre exact au dessus du r sum de chaque rapport Les rapports techniques sont r sum s dans la revue R sum s des sciences aquatiques et halieutiques et ils sont class s dans l index annual des publications scientifiques et techniques du Minist re Les num ros 456 de cette s rie ont t publi s titre de rapports techniques de l Office des recherches sur les p cheries du Canada Les num ros 457 714 sont parus titre de rapports techniques de la Direction g n rale de la recherche et du d veloppe ment Service des p ches et de la mer minist re de l Environnement Les num ros 7 15 924 ont t publi s titre de rapports techniques du Service des p ches et de la mer minist re des P ches et de l Environnement Le nom actuel de la s rie a t tabli lors de la parution du num ro 925 Les rapports techniques sont produits l chelon r gional mais num rot s l chelon national Les demandes de rapports seront satisfaites par l tablissement auteur dont le nom figure sur la couverture et la page du titre Les rapports puis s seront fournis contre r tribution par des agents commerciaux Canadian Technical Report of Fisheries and Aquatic Sciences 2037 1995 SOFTWARE TO COMPLEMENT HTI S MODEL 240 SPLIT BEAM ECHOSOUNDER A USER S GUIDE TO HAFU HYDRO ACOUSTIC FILE UTILITIES AND QTS QUALARK TOOLS FOR S PLUS Norm Olsen of
31. ed by HAFU into S Plus binary format This step is necessary before any plots or summaries can be produced since S Plus can only work with it s own format of data file Enter the name of the source data file and a name for the target data frame data frames are a particular kind of S Plus data set Example REX XXE ER REX KE EAN XX A ER ON XX OX XX OX OX XX SCAN A DATA FILE INTO A DATA FRAME IBSZZZEERSEEERERERRERSERERSERSERRSEERSSEREEZS Enter a name for the target data frame a244 fsh Enter the source file name give full path c 94sysl results a2440000 a1f B 2 3 Remove noise from a data frame This item allows you to remove echoes from a data frame using visual tools This is useful for eliminating rocks or other non fish targets The display consists of two windows one titled brush that shows selected variables from the given data frame 19 plotted against each other and one titled spin that shows any three of these variables in a 3 D plot that can be rotated and expanded Use the left mouse button to highlight any echoes that you wish to remove from the data A small box in the lower right of the display lists the target strength in decibels of all echoes displayed As you highlight echoes with the mouse the corresponding target strength is highlighted in this box This is useful for checking the target strength of individual echoes Fig 17 shows a display of this routine See S Plus documentation for more informatio
32. fications to the way that the SUMMARY file is written However you can stil use this procedure provided that your SUMMARY files summarize all of the data collected on a specific day and only the data for that day B 2 7 View Results This item executes the shareware program called LIST in the RESULTS directory under the current working directory This allows you to view any of the results from your HAFU session by positioning the highlight bar over a file name and pressing ENTER You can also perform several file management activities from within LIST Refer to the LIST documentation or press the F1 key from within LIST for more information B 2 8 Shell to DOS This item allows you to temporarily exit HAFU and access the DOS command line When you are ready to return to HAFU enter EXIT B 2 9 Quit This item quits HAFU and returns you to the operating system CHAPTER 2 QTS QUALARK TOOLS FOR S PLUS A OVERVIEW QTS is a collection of S Plus routines that we developed while working at our hydroacoustic site near Qualark Creek on the Fraser River just north of Hope These tools are primarily designed to graph data but they also provide options for producing summaries of fish passage and for editing data interactively QTS is written in the S language and requires the Windows version of S Plus to run full description of the S language is given in Becker et al 1988 Like HAFU QTS provides a menu driven interface You ca
33. h and the ability to track and enumerate salmon as they migrate upstream to their spawning grounds We have been using this system extensively since 1993 at a site near Qualark Creek on the Fraser River just north of Hope British Columbia Canada During this time we have developed several software packages to help us deal with the large volume of data produced by the system and to aid us in analyzing and processing these data The software is grouped into two categories file management utilities including utilities to compress concatenate and convert HTI data files and data analysis routines focusing primarily on graphical representations of the data These categories are presented here as HAFU Hydro Acoustic File Utilities and QTS Qualark Tools for S Plus respectively HAFU is a DOS program and requires no special hardware or software to run QTS is written for S Plus for Windows and therefore requires Windows 3 1 and S Plus for Windows A floppy disk containing the software discussed in this document can be obtained from us free of charge Vili R SUM Olsen N 1995 Software to complement HTI s model 240 split beam echosounder A user s guide to HAFU Hydro Acoustic File Utilities and QTS Qualark Tools for S Plus Can Tech Rep Fish Aquat Sci 2037 45 L chosondeur faisceau divis mod le 240 de l Hydroacoustic Technology Inc HTI est l appareil la fine pointe de la technologie en mati re d hydroacoust
34. he program expects file names to be in a specific format If you wish to use HAFU you must follow these naming conventions or else obtain a modified copy of HAFU from us The naming conventions are as follows Table 1 File naming conventions used in HAFU File Type Naming Convention Extension HTI RAW SDDDHHMM RAW Concatenated HTI RAW SDDDHHMM RW2 PBS RAW PDDDHHMM ALR HTI ECHO SDDDHHMM ECH PBS ECHO PDDDHHMM ALE HTI FISH SDDDHHMM FSH PBS FISH PDDDHHMM ALF HTI SUMMARY SDDDHHMM SUM HTI INTEGRATION SDDDHHMM INT Compressed HTI Files YYSDDD ZIP Where A letter that refers to the echosounder system on which data were DDD MM YY collected A System 1 B System 2 A letter that refers to the port on which the data were collected A Port 1 B Port 2 Note that this can cause some confusion with the S convention used for HTI files which refers to system number In general you should keep data from each system in separate locations The day of the year on which the data were collected beginning at 1 on January 1st of each year and ending on the last day of the year usually 365 We define this as the Julian Day although Julian Day is not technically defined this way The hour that the data file began based on a 24 hour clock starting at 00 at midnight of each day and ending at 24 at midnight on the next day The minute that the data file began from 00 to 59 The year that the data were collected on e g
35. ique faisceau divis Les appareils faisceau divis pr sentent plusieurs avantages par rapport aux chosondeurs classiques dont la possibilit d estimation pr cise de l intensit des cibles et des possibilit s de rep rage et d num ration des saumons migrant vers l amont jusqu leur fray re Nous avons abondamment utilis ce syst me depuis 1993 un emplacement situ sur le Fraser pr s du ruisseau Qualark juste au nord de Hope Colombie Britannique au Canada Pendant cet intervalle nous avons mis au point plusieurs progiciels facilitant la manipulation des imposants volumes de donn es produits par le syst me ainsi que l analyse et le traitement de ces donn es Les logiciels sont regroup s en deux cat gories des utilitaires de gestion de fichiers incluant des utilitaires de compression de concat nation et de conversion de fichiers de donn es HTI et des sous programmes d analyse de donn es ax s principalement sur la repr sentation graphique de ces donn es Ces deux cat gories sont ici respectivement d sign es par les acronymes HAFU Hydro Acoustic File Utilities et Qualark Tools for S Plus Le HAFU est un programme DOS et son ex cution n exige aucun mat riel ou logiciel sp cial Le QTS est crit pour le S Plus pour Windows et son ex cution exige donc le S Plus et le Windows 3 1 Nous fournissons sans frais une disquette comportant les logiciels ici pr sent s 1 INTRODUCTION This report is a
36. item B 2 5 Directory of data frames This item lists all available data frames data objects that can be passed as arguments to the various plotting routines Example e e e dece e eee ee eee ee eee eee ee ke e ee eee fe e e x DIRECTORY OF AVAILABLE DATA FRAMES 3k e ee oe e eee eoe eee e eoe ee eoe e e ee eee eode data class storage mode extent object size dataset date CURRENT ECH data frame list 9263 x 16 1268743 95 01 09 15 42 CURRENT FSH data frame list 1076 x 22 199030 95 01 09 15 42 CURRENT RAW data frame list 13360 x 15 1726472 95 01 09 15 42 a244 ech data frame list 9263 x 16 1268743 95 01 09 14 02 a244 fsh data frame list 1076 x 22 199030 95 01 09 14 03 a244 raw data frame list 13360 x 15 1726472 95 01 09 14 50 newa244 fsh data frame list 970 x 22 179449 95 01 10 9 05 B 2 6 Make a RAW object current This item allows you to make a RAW data frame the current RAW data frame Use this procedure when you wish to pass the same RAW data frame as an argument to several different routines without having to retype the name of the data frame each time This only applies to routines that use a RAW data frame as a default argument 222 2 B 2 7 Make an ECHO object current This item is the same as B 2 6 but applies to an ECHO data frame B 2 8 Make a FISH object current This item is the same as B 2 6 but applies to a FISH data frame 23 B 3 The Images Menu B 3 1 Z vs Y This item produces a
37. k TARGET DISTRIBUTION BY VERTICAL AND HORIZONTAL ANGLE ok ck ce ce e ke e e oe e e ce oe e ce e ke e ke che ce ke ce ce oe oe oe ecce e ce ce ce e ce e ee ke ce ce e ce e ce oe ce e ce e e e ok v ko Enter data frame to plot default is last ECHO scanned a244 ech Enter title for plot Day 255 Vertical and Horizontal Target Distribution Day ass 00 Vertical Distribution a o lt a i a ra s iI lt a GL I ILE IEE ELIE LS LE DL OE ATE TE TE EN 0 10 20 30 40 50 60 Frequency Horizontal Distribution 9 B E Bm _ 5 0 5 10 Horizontal Angle Fig 24 Histograms showing target frequency vs vertical angle degrees and target frequency vs horizontal angle degrees 29 B 4 3 TS vs off axis angle This item produces histograms of target strength in decibels for each degree of off axis angle spanned by the data Fig 25 Note that this plot is only appropriate for beams with circular cross sections Example K HISTOGRAMS OF TARGET STRENGTH PER OFF AXIS ANGLE fe ce cde ce oe ce ce he ce ede cde echec che e he ede bee ce e hee ce he de ce e che he ce eee e KKK Enter data object to plot Enter title for plot Echo Data 1to tagi arg ideo tagi Tiegh jug 5 to 6 E Yhis 4 to 5 Ti E ragi High di
38. mm dd yy Where mm dd yy the calendar date in the format month day year e g gt date2jd 07 20 95 The Julian Day on 07 20 95 is 201 44 REFERENCES Becker R A John M Chambers and Allan R Wilks 1988 The new S language a programming environment for data analysis and graphics Wadsworth and Brooks Cole California 702p Hydroacoustic Technology Inc 1933 Model 240 split beam digital echo sounder operator s manual ver 1 03 Hydroacoustic Technology Inc Seattle Washington 72p Peterson T S 1960 Calculus with analytic geometry Harper and Brothers New York 487 488 45 ACKNOWLEDGEMENTS Ithank the following people in alphabetical order for their many suggestions that helped in the design and implementation HAFU and QTS George Cronkite Hermann Enzenhoffer Sam Johnston Dr Robert Kieser and Dr Tim Mulligan
39. move noise from a data frame Generate a passage report Directory of data frames Make a RAW object current Make an ECHO object current Make a FISH object current Leave this menu Access QTS Help File Select one View online help Data manipulation Images Histograms Echograms and tracke Quit TS vs off Axis angle Leave this menu Quit QTS Select one Select one Simple echogram noo Echogram examiner Target track examiner Leave this menu Upjdown tracks by range Targets by vert horiz angle TS vs off axis angle TS vs range Leave this menu Fig 14 Overview of the QTS menu structure Graphics 2 Current Histogram of tracked fish vs range Test REKKLEKR LENE GERE IE AC ACIE BEEN EE DE IE AE DE DE NN ME MER HISTOGRAM OF UPSTREAM AND DOWNSTR GC JE 3E DE 3E 3E 3E 3 JE E JE JE 3 3 diEnter FISH data frame to plot defa Enter direction of water flou left 1 is left to right Enter title For plot Test 32 as 4n 43 Pare jme Select one Up down tracks by range Targets by verthoriz angle TS vs off axis angle TS vs range Leave this menu Fig 15 The layout of S Plus for Windows when QTS is running Note the command window graphics window and QTS menu B QTS USER S MANUAL B
40. n access this menu by double clicking on the QTS icon in the Program Manager of Windows just as you would any Windows application Double clicking on the icon launches S Plus for Windows and executes the appropriate S code to initialize the QTS menu Fig 13 shows the QTS icon in a program group with other application icons dioacousties 18 x PES QTS Help HAFU WinZip Fig 13 The QTS icon in a Program Manager group When the QTS main menu appears activate a menu item by double clicking on the menu item text For example to view a Windows help file concerning QTS double click on the text that reads View on line help To leave a sub menu and return to the main menu double click on the text that reads Leave this menu There is only one level of sub menu under the main menu so selecting Leave this menu will always return you to the main menu The complete menu structure of QTS is shown in Fig 14 In addition to the QTS menu S Plus also displays a graphics window and a command window The graphics window displays various graphs selected from the QTS menu such as histograms and images The command window displays text messages and prompts and also accepts text input Most of the QTS menu items require that you enter some information into the command window such as the names of data frames and labels for plots Fig 15 shows the S Plus display when is running 15 Date Manipulation Select one Re
41. n on using the brush spin display Example ck coke coke eco OX XX XX REMOVE NOISE FROM A DATA FRAME XX R REX XX XX KEK Enter a name for the target data frame newa244 fsh Enter the name of the source data frame a244 fsh rd Cho M Persistence Labels C Big Points sellis pi eet IH mp Range TS Speed Y Coord Mertical X Coord Fig 17 Screen display of the brush and spin plot from the Remove noise from a data frame menu option 20 B 2 4 Generate a passage report This item generates a table output to an Excel spreadsheet of upstream and downstream passage per hour for a given time frame Table 2 The data are also displayed graphically Fig 18 This is a useful tool for producing daily summaries of fish passage through the beam The count is automatically expanded for the portion of each hour that the beam was not operated For example if two beams were multiplexed at 15 minute intervals each beam would collect data for 30 minutes out of each hour This procedure multiplies the count in each beam to make an estimate of the total number of fish that passed through the beam each hour Thus the count would be expanded by a factor of 2 for a beam that operated for 30 minutes out of each hour The direction of water flow past the beam must be entered so that upstream and downstream passing fish can be correctly identified Water flow direction is
42. o mui 485 Fig default is last ECHO scanned hisz 3to3 0 ragi High ide Mis 6 to 7 ragi Siargjh deo au 2 a m a244 ech Sto 4 E gt tag ey 7 to 8 0 i w m Fuga Hieghid 25 Histograms of target strength dB for each degree of off axis angle spanned by the data 30 B 4 4 TS vs range This item produces histograms of target strength in decibels for each meter of range spanned by the data Fig 26 Example c ce ce ce checked ce oce ke ke ce che che ce ce coke oe ce ce coke cde ke che ce HISTOGRAMS OF TARGET STRENGTH PER METER RANGE ck c cce e ke ce nece ke ee ce cde ce ce cec ce ce coche ce eec e ce ce ke ce ce ke ek ck ck ck kk kk ok ko ox Enter data object to plot default is last ECHO scanned a244 ech Enter title for plot Echo Data Fuge Mirgh en ty Faq Oey 20 70904 Eces Range 3 to 4m Range 4 to 5m Range 5 to 6m Range 6 to 7m L ss n M m a ELI EI m 3 m gt 2 ragi dio rapi Siri 90 rap Mirgh doo Range to Range 6 to Im 1 eee a 4m ragi Sevghi ram 165 Fig 26 Histograms of target strength dB for each meter of range spanned by the data ee B 5 The Echograms and Trackers Menu B 5 1 Simple echogram
43. ocessoccsovs esecsoscsoccone CCEETEELEEEL EE sessccscoscenos sesoocvecceceoe CELEELECET EEE seocvocsosocvos eecsocovseveoevs secsecccceevoos CEELELEPEEL TES esececeocevoee eceovosovecvoen Woman LR iv B 2 4 Generate a Passage B 2 5 Directory of Data Frames B 2 6 Make a RAW Object B 2 7 Make an ECHO Object Current B 2 8 a FISH Object Current B 3 The Images B3 D de diet PP PNE BST M idque aret be vd p ist X V8 M 3 4 TS vs Off Axis Angle ss B 4 The Histograms Menu B 4 1 Up Down Tracks by B 4 2 Targets by Vert Horiz Angle B 4 3 TS vs Off Axis Angle BAA TS vs Range aiio cessi cot Fart e e ipea credens B 5 The Echograms and Trackers B 5 1 Simple EchOBram B 5 2 Echogram Examiner B 5 3 Target Track Examitiet uiui 1t rete geie Appendix A DATA F
44. ow of File compression verification screen Convert HTI RAW files to PBS RAW file verification screen The RESULTS directory with two PBS RAW files listed The status window upon completion of PBS ECHO file to PBS FISH Hil CONVETSION 5 semer ane The QTS icon in a Program Manager Overview of the OTS menu structure The layout of S Plus for Windows when QTS is running The OTS help System DS inne to visita boe EEG Screen display of the brush and spin plot from the Remove noise from a data frame menu option Plot produced by the Generate a passage report menu option Z vs Y density Image enter ne trees ZVS X density Image oa existe pe tutu teils trat ed ege X vys Y density imag anne Target strength vs off axis angle density Histogram of upstream and downstream tracked targets TAN Be eT Histograms showing target frequency vs vertical angle degrees and target frequency vs horizontal angle degrees Histograms of target strength dB for each degree of off axis angle spanned by the data Histograms of target strength dB for each meter of range spanned UJ Vi LIST of TABLES Table 1 The function of each menu item in HAFU
45. ption of each menu item is available via this window B 1 5 The Read Window HAFU uses the shareware program called LIST to display various ASCII files including HTI and PBS data files A full description of LIST s features are not included in this discussion Refer to the LIST documentation in the HAFU LIST directory for more information regarding it s use B 2 Menu Items B 2 1 Compress Daily Files This menu item is used to compress all HTI files for a given day of a given year into a single file To begin this procedure enter the number of the echosounder system and the year and day that the HTI files were collected The echosounder system number indicates which system the data were collected on Currently it can only be 1 or 2 as an historical consequence of our use of two echosounders at Qualark If you use only one echosounder system the system number will always be 1 If you use more than 2 systems contact us to have your version of HAFU modified The year must be entered as 4 digits for example 1995 The day is defined as a sequence starting at 1 on January 1st of each year It must be entered as 3 digits for example 013 for January 13th When you have finished entering all the required information verify your entries by pressing Y after the Is the above correct Y N prompt If you wish to change one or more of your entries press N after this prompt Once you have verified your entries HAFU searches the current di
46. rectory for all HTI files that match the system year and day that you specified and compresses them using PKZIP into a single file While this is happening the display switches to a plain DOS screen that allows you to view the compression as it occurs When compression is complete the resulting file is checked for errors by PKUNZIP and the results are displayed on the screen You can use the Page Up and Page Down keys to view these results and look for any compression errors that may have occurred Each compressed file is listed down the left side of the screen with either an to the right of it or an error message Fig 9 Press ESC when you have finished viewing this information The display then switches back to HAFU and you are asked if you wish to delete the original HTI files Press Y if you are satisfied that the file compression operation was successful i e if no error messages were displayed or N if an error occurred If errors were encountered you may wish to retry the compression procedure or quit HAFU and take other steps Compression errors are very rare in fact we have yet to encountered one while working with our data the error shown in Fig 9 is a simulation 10 PKUNZIP R FAST Extract Utility Version 2 04g 02 01 93 Copr 1989 1993 PKWARE Inc All Rights Reserved Registered version PKUNZIP Reg U S Pat and Tm Off _ 80486 CPU detected _ EMS version 4 00 detected XMS version 2 00 detected DPMI ve
47. ree dimensional position of a target Therefore it is possible to accurately track and enumerate fish as they migrate through the echosounder beam The receiver contained in the split beam echosounder provides simultaneous 20 log R and 40 log R time varied gain TVG output so echo integration and target tracking can be accomplished concurrently The digital split beam processor DSBP board processes signals received from the split beam echosounder This board interfaces with the 486 computer attached Hydroacoustic Technology Inc Seattle Washington USA 395 to the echosounder via a standard ISA slot The 486 computer also runs HTT s real time software and stores data files collected during echosounding The digital chart recorder located in the echosounder prints echograms using a standard 24 pin dot matrix printer Echogram printing is controlled through a menu system accessible via the keyboard and monitor attached to the echosounder The keyboard is also used to input various echosounder settings such as time varied gain and ping rate The digital audio tape DAT recorder records raw echosounder output on tape If desired tapes can later be re processed through the DSBP using modified echosounder parameters The oscilloscope provides the primary feedback for aiming the acoustic beam It displays the return signal voltage vs time in effect the return signal strength vs range The rotator control remotely actuates a
48. rocess RAW data using HTI s DSBP software This software will accept any HTI RAW file and re track the data creating ECHO FISH and SUMMARY files as output This procedure can be very time consuming when one is dealing with dozens of RAW files The menu item Merge HTI RAW files is designed to expedite reprocessing of HTI RAW files by concatenating all HTI RAW files that fall within a user specified time frame The concatenated files are split into separate files for each port and a new set of files is produced each time a change in a parameter value is encountered in the original HTI RAW files This can greatly reduce the number of HTI RAW files you must deal with and also provides a clear indication of when a parameter change occurred For example suppose you have six HTI RAW files representing data collected from two ports over a period of six hours and that the same parameters were used to collect all of these data The Merge HTI RAW files procedure will create two HTI RAW files from these data one file containing the data from port 1 and one file containing the data from port 2 As with previous menu items you must enter the system number year starting and ending day and starting and ending times HAFU then searches the appropriate compressed files for HTI RAW files that fall within the period specified he B 2 6 Display Upstream Tracked Fish Counts This item is not yet implemented as it requires that HTI make some small modi
49. rotator to which the transducers are attached This allows positioning of the beam both vertically with respect to the river bottom and horizontally in the up stream or down stream direction SOFTWARE HTI provides real time and post processing software that reside on the 486 computer connected to the echosounder Integral to this group of programs are DSBP which performs echo integration and DSBPTRAK which performs target tracking These two programs multitask under the DesQView operating environment processing output from the DSBP board and producing output in the form of ASCII data files and real time graphical displays A variety of graphs can be displayed while data are collected Fig 2 Fig 2 START END BOTTOM TRACKING GRAPH ROTATE 3D PRINT PLOT MAIN MENU Tracked Fish by Range Target Strength TS Bins dB 0 0 6 0 12 0 Current Output Files A2411600 RAW A2411600 ECH A2411600 FSH Real Time Results Echoes 1 Tracked Targets 35 Average TS 29 2 dB Current Settings Run Not Specified Bottom Range 11 0 meters Port 2 Example on screen display of HTI s DSBP software Several real time graphical displays are available This one shows a histogram of tracked targets by range ee CHAPTER 1 HAFU THE HYDRO ACOUSTIC FILE UTILITIES A OVERVIEW Although HTT s software is necessary for real time data acquisition and analysis we have found that their post processing software is cumbersome to use with
50. rsion 0 90 detected Searching ZIP 94A238 ZIP Testing A2380000 RAW PKUNZIP W15 Warning file fails CRC check Testing A2380000 ECH Testing A2380000 FSH Testing A2380000 INT Testing A2380100 RAW Testing A2380100 ECH Testing A2380100 Testing A2380100 Testing A2380200 Testing A2380200 Testing A2380200 Testing A2380200 TE Fig 9 File compression verification screen An error is shown for the first file compressed B 2 2 Convert HTI RAW files to PBS RAW file This item converts all HTI RAW files that fall within a user specified period into a PBS RAW file See appendix A for a full description of the RAW file type To begin this procedure enter the system number 1 or 2 the start and end day and start and end times of the data you are interested in Times must be entered as 4 digits representing the hour and minute on a 24 hour clock starting at 0000 at midnight and ending at 2400 at midnight the next day Once your entries are complete verify your choices by pressing Y or N after the Is the above correct Y N prompt Fig 10 shows an example input screen after the user has entered all required information and is being asked to verify that the information is correct Input ESC to cancel System 1 1994 Start Julian Day 231 End Julian Day Start time 2230 End time Y N 15 the above correct Fig 10 Convert HT RAW files to PBS RAW fil
51. th Frequency by Ott Axiz Angle Day 255 Tracked Echoes Density Image OA Aag le 20 Target Strength dB Scatter Plot Orhan Aigle 20 Target Strength dB Fig 22 Target strength vs off axis angle density image 29 B 4 The Histograms Menu B 4 1 Up down tracks by range This item produces a histogram of tracked targets by range in meters Fig 23 Upstream migrating targets are shown above the x axis downstream migrating targets are shown below the x axis Only FISH data frames may be used with this routine Example e e ce e eee ce eee e ce e de dee eee eee ee oe che e e e e e de e ee de dee e de de ee de de e ede he ce ee he eee e e ee e X HISTOGRAM OF UPSTREAM AND DOWNSTREAM TRACKED TARGETS BY RANGE RRRRRRRRERAARRRRRRRRRRRR A RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR RRR R R Enter FISH data frame to plot default is current a255 fsh Enter direction of water flow left to right or right to left default is left to right left to right Histogram of tracked fish vs range Day 255 Upstr gt c 5 oF a u Downstream 3 0 3 5 4 0 4 5 5 0 5 5 5 0 6 5 7 0 7 5 8 0 8 5 Fig 23 Histogram of upstream and downstream tracked targets by range 28 B 4 2 Targets by vert horiz angle This item produces histograms of target frequency vs vertical angle and horizontal angle in degrees Fig 24 Example c e ce kK kkk kkk de cde ke kok kok eode ce kok kok ko
52. to collect data on port 1 B Section listing parameter values used to collect data on port 2 C Section listing data collected and times when port switching occurred The contents of the HTI RAW file are listed in Table 1 35 Table 1 Contents of the HTI RAW data file Column Heading _ Contents Ping Number e Sequential ping number since the file start time Range meters e Range of target in meters from the face of the transducer Sum Chan Volts Peak output voltage summed over all 4 quadrants of the transducer 6dB P W e Pulse width at 6dB from peak voltage 12dB P W e Pulse width at 12dB from peak voltage 18dB P W e Pulse width at 18dB from peak voltage Up Dn Angle e Horizontal position of target in degrees to the left or right of the vertical axis Lf Rt Angle e Vertical position of target in degrees above or below the horizontal axis Mux Port e Multiplexer port on which data were collected 2 PBS RAW FILES HAFU uses the parameter values for each port to calculate several additional fields The parameter values are then discarded An example of a PBS RAW file is shown in Fig 2 time ping x y z range pw 285 0 016194 563 0 1864 0 1208 3 1522 3 1600 0 000208 285 0 016222 564 0 1789 0 1528 3 1512 3 1600 0 000146 285 0 016250 565 0 1250 0 1618 3 0632 3 0700 0 000167 285 0 016306 567 0 4669 1 1235 10 2782 10 3500 0 000167 horiz phi theta scv bpf ts 3 3843 4 0310 147 0509 0 5359
53. urrounding each point represent the relative target strength of each returned echo The 3 bottom plots mirror the top ones but include a user specified buffer period in seconds before and after the period during which the target was tracked On these 3 plots the symbol represents echoes that were returned during the tracked target s passage plus the buffer time but that were not identified as belonging to any tracked fish The symbol represents echoes that were tracked but that belong to targets other than the currently displayed one Example KEKE KKKKKKKKKKKKKKKKKKKK e e e EXAMINE TRACKS TARGET BY TARGET fe e ce eoe e ee dee ce ee eee ee cfe eee e dee eee oe ee e k Enter RAW data object default is last scanned a244 raw Enter ECHO data object default is last scanned a244 ech Enter starting fish number optional default 1 35 Enter buffer time in seconds optional default 2 2 Enter beam width in degrees optional default 8 8 Y vs X Beam Cross section Z vs X Beam top down view Xvs Ping Number Y Height qn X Ups team n Downstream X Upsweam n Dowsstream 3 A 0 1 a 301 X Upstream m Downstream Z Distance from transducer m Ping Number Y vs X Beam Cross section Z vs X Beam top down view X vs Ping Number Y egit qo X Upstream qi Dowastream X Upstream qu e Dots trezm 2 1 0 00 05 10 8 78 8 82 8 86 8 90 3000 3005 3010 3015 X
54. ut File end times period specified lt muxzoutput gt Convert HTI Year days ofthe PBS format echo file echfiltr Echo Files to year and start and containing all HTI Echo file HTIechofile PBS Echo File end times data for period specified muxloutput lt mux2output gt Convert PBS Name of PBS echo PBS format fish file containing ech2fsh lt echofile gt Echo File to PBS file conversion of specified PBS lt fishfile gt Fish File echo file Merge HTI Raw Year days of the HTI format raw files split into None Files year and start and output for each multiplexer end times port New files are written each time a parameter change is encountered View output files from any of list the above procedures This item launches the shareware program called LIST View Results None Shell to DOS None Exits temporarily to DOS command Type exit to return to HAFU uit None uits HAFU Not applicable The primary value of HAFU is its ability to deal efficiently with large amounts of data from numerous files For example during an operational day at Qualark the echosounder may produce up to 120 separate data files 5 file types x 24 hours equaling on a low passage day perhaps 10 megabytes of data Using HAFU the user can compress all of these files into a single file approximately 10 30 of the original size HAFU then operates from the compressed file avoiding the need to decompress the files directly For instan
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