HP OPD User Manual - Mote Marine Laboratory
Contents
1. OPTICAL PHYTOPLANKTON DISCRIMINATOR OPD USER GUIDE HIGH PRESSURE MODEL VERSION 1 4 FEBRUARY 11 2011 Mote Marine Laboratory 1600 Ken Thompson Parkway Sarasota Florida 34236 941 388 4441 Phytoplankton Ecology Program CONTENTS CONIINI c 2 DOCHOn A General IBIOPRRITONH e ois eoi Reap I Op x au nes 3 1 1 General DeSCrip ME 3 EM 4 1 3 Contents of Shipping Case oon or i e Eo BS 4 Section 2 Operations and Maintenance 5 2oh COPD Internal E 5 2 2 Connections and Establishing Communicatons 8 ZS ADE DC DIEI EET TE T TU T UM 12 BASIC IT NSA EE 13 2 4 Replenishing the CDOM Reference supply 0000ieeeneneennnsnsssssssssseeeee 14 2 5 Purging Air from the System cccccccccccccecccceeseseeecceeeeesaaeesseeeeeees 14 2 6 Testing and Operating the Instrument 15 2 7 Downloading Data EE 17 2 9 Results Folder EI 17 2 9 Filter Replacement nionee ieee RUNE NEUE 18 2 10 RKeassembhne OPD eeraa EE 18 SOGHOIn o GHAET E 27 S Ghd r TEE 22 3 2 Downloading Data Files from ODD 24 3 3 Installing the OPD Leak Detection Cable 27 DOCIOH A APPENA COS cca E Cone Eoi aes ot omi uon aep UAE Fb Con ae t 29 Appendix A E E 20 Appendix B Replacement Darts 30 Appendix C Configuring Glider files for operations with OPD 31 Appendix D Configuring glider for OPD parameter reports 3l Appendix E Installing OPD2. Drive D t login exp ZER Exports Library File 12 10 2007 12 00 AM S Removable Disk E longterm dat KB DAT File 12 10 2007 12 00 AM 3 w LIMIT 055 I mbalist dat 1 KB DAT File 12 10 2007 12 00 AM CH app shlist dat 1 KB DAT File 1z 10f2007 12 00 AM B BIN sensdata dat tupe DAT File 12 10 2007 12 00 AM C config SIMUL SIM Date Modified 12 10 2007 12 00 AM 1120 2006 2 45 PM CO Los zmext dat Size 303 bytes 12 10 2007 12 00 AM Lj mafiles rg Edit the SIMUL SIM file as required to read 23 Simul sim fon bench just electronics 5 Replace the glider flash card and remove and read the Science flash card Here is an example of the root directory of Science a 1 4 File Edit view Favorites Tools Help Q Back a yo Search Wey Folders sre E A Mame Size Type Dake Modified P File and Folder Tasks app File Folder 11 25 2008 3 47 PM bin File Folder 11 25 2008 3 47 PM config File Folder 11 25 2008 3 47 PM File Folder 11 25 2006 8 56 PM autoexec bat 1 KB PM5 DOS Batch File 12 10 2007 12 00 AM MOTELO GI TXT IB KB Text Document rilz ne 6 08 PM CH Make a new Folder es Publish this Folder to the web KT Share this folder Other Places 3 My Computer 6 Here is the content of the Science config folder config File Edit View Favorites Tools Help SE S e Search Folders Address BI ce A Mame Size Type Date Modified File and Folder Tasks A E PROGLETS DAT
3. Replacement The hollow fiber filter used in OPD has a maximum rated trans membrane pressure of 15 psi The an parameter ByPass Pressure reports that pressure y across the filter in the Status Message for every cycle After many cycles bypass flushing and CdomRef cleaning will still leave the filter membrane permeability too low It must be replaced at or before the pressure exceeds rating during operations A A A spare filter has been included in your spare parts kit See Appendix B for replacement parts information 2 10 Reassembling OPD Reconnect the DB 9 connector from OPD to Science and reconnect the OPD power cable to its connector as depicted in section 2 2 18 2 Place CDOM reference bags inside the CTD ring 3 Make sure the tubing will not be crimped or pinched when replacing the hull old the fluid bags in place 5 Replace the hull Aligning the engraved index marks on the ypper and lower part of the hull with the ring index marks will assure bolt hole alignment for the aft ring 19 Replace the aft ring Secure it to the chassis frame with the hex nuts removed earlier Apply only a light torque For G2 glider configured OPDs see appendix J Thread the Peek sample port tubes through the ring openings and carefully slide the plastic tubing to port nut metal compression ring and rubber ferrule in that order onto the tubing The flattened end of the compression ring must
4. above If no error or only one error condition exists the Status code is O or is the Hex value of the single error and interpretation 1s direct and simple For combined errors decoding the reported Status code requires converting the Hex value of Status to Binary then determining which bits of that binary value have the value of 1 and correlating those bits with the above listed error types An online converter such as http www easycalculation com hex converter php may be helpful It s also possible to deduce which combinations of errors are encoded in the Status code by adding various combinations of Hex values assigned to the errors For example a deuterium light failure 0x80 combined with a leak OxO1 results in a reported Status code of 81 Even without the step of the binary conversion to 0010000001 it s clear that code 81 could only result from the combination of these two codes 0x80 and 0x01 40 Appendix I OPD CONFIG TXT descriptions e CorrWaveMin 400 The lower end of the wavelength range in nm over which the Similarity Index is evaluated e CorrWaveMax 700 The upper end of the wavelength range over which the similarity Index is evaluated e AbWaveMin 390 The lower end of the wavelength range over which CDOM absorption 1s evaluated e AbWaveMid 440 The wavelength value where CDOM absorption is reported e AbWaveMax 490 The upper end of the wavelength range over which CDOM absorption 1s evaluated
5. face towards the nut with the narrow end of the rubber ferrule towards the sharp edge of the ring Ensure that the sample port base has the size 012 o ring still captive in the groove on the bottom Ensure all o rings are undamaged lightly lubricated and that all o ring seating surfaces are clean Insert the ferrule tubing assembly into the sample port base Hold the tubing flush with the end of the rubber ferrule while finger tightening the sample port base to the nut Finish with a light torque of the base while gripping the nut with pliers 20 10 Rotate the sample port base so that its channels are facing aft as shown below and then insert the tubing to port nut into the opening in the ring seating its o ring Channels aim aft 11 Assemble the copper mask to the transparent port cover with the oval opening positioned above the water channel in the cover as shown in the figure 12 Clean and reassemble the filter screen to the transparent port cover on top of the copper mask ke 13 Assemble this cover assembly to the port base aligned so that the oval opening in the copper mask rests above the channels in the base clamping the screen mesh between them Secure with the 8 32 socket head cap screws 2 Section 3 Glider Operations 3 1 Glider Ops l When the OPD is ready to be used in the Glider position it gently on the glider cart being careful with the sample ports Position the instrume
6. optical absorption effects from the measurements of the unfiltered water during the analysis of the optical data CDOM Reference is a mixture of 3 parts filtered sample water with 2 parts 1N HCI solution A supply of this fluid is used to periodically clean the LWCC lumen and to adjust the settings of the instrument Cell is an OPD configuration for using a cell phone modem for communications Dark refers to a Spectrometer measurement run without light Dark Pixel readings are subtracted from illuminated readings as an instrument compensation step on every cycle Discriminate refers to the part of the measurement cycle where the raw unfiltered water sample is optically measured Debug is an optional OPD program feature that sends detailed progress information for each cycle to the computer console and the DEBUG TXT log file Nohost is an optional OPD program feature that automatically starts measurement cycles In this mode of operation once started OPD runs autonomously for as long as electrical power is provided Polled is an optional OPD program feature that keeps OPD awake for as long as 5 minutes after completing a cycle while awaiting a host to poll it for its status message Once it reports status it goes to sleep or proceeds with the next cycle Similarity Index SI Research has shown that the phytoplankton species K brevis can be discriminated from other bloom forming species based on 29 12 13 analyses of its opt
7. travel status port select valve position CDOM reference mL remaining and time 12 Basic HP OPD Commands Liehtson Turns the D2 light on tungsten and deuterium sources Deuteriumon Turns only the Deuterium light source on Selects Filter channel for water sample ungsten on Reference Pump Off Turns CDOM reference pump off Sample Pump On __ Turns sample pump on Override On Override Off After clearing the end of travel optodetector at syringe end stop turn override off Reverse Sample Once syringe pump reaches an end of stroke and parks this command reverses it Pump and sends it to the opposite end stop Valve Toggle Instructs valve to switch to other port Status Report Reports the current OPD status message Makes reference pump run forward and then reverse multiple times This is used mainly to run cleaning solutions through the system Other commands may also appear in your left hand menu Additional opcode and other advanced commands are listed in Appendix F These commands should be under the direction of a factory service technician 11 Once the cycle has stopped under Reports click on the Sampling Setup and Status Reports The settings reported should be validated before initiating actual bench or field measuring cycles To change the parameters seen in the Sampling Setup or Sensors Reports under the Setup heading in the left side of the screen select the parameters to be changed A pop
8. up box for the parameter selected will appear on the screen for entry of the desired value Example cycles to do 13 Enter Parameter Value Enter substitution for first H in numbercycles gt Enter a value and click ok 2 4 Replenishing the CDOM Reference supply l 3 Disconnect the luer lock fitting from the fluid bag labeled CDOM Reference supply To refill use a luer syringe or tubing fitting that will fit one of the two luer fittings on the bag The CDOM Reference fluid should be filled from a pre mixed solution comprised of 3 parts of 0 22um filtered water preferably from the body of water the instrument will be sampling in and 2 parts IN HCI 1 Normal Hydrochloric acid The maximum volume of fluid the bag can hold once placed in the instrument is 350 mL Please do not exceed this amount Remember to manually reset the value of CDOM Ref Supply mL to 350 in the OPD parameters 4 Once fluid has been added purge the bag of all air and re connect to its tube 2 5 Purging Air from the System l In the parameter menu in Setup turn Reference pump on This will pump CDOM reference fluid from its supply bag to the waste bag by way of some of the instrument s fluid circuits Operate the pump while watching for bubbles released into the waste reservoir Operate until the bubbling ends Select Reference pump off Select Reverse Sample Pump The syringe pump will begin to move the syringe plungers pushi
9. 38KB DAT File 11 3 2008 3 21 PM amext dat 2KB DAT File 12 10 2007 12 00 AM cJ Make a new Folder GG Publish this Folder to the Web KT Share this Folder Other Places fog SCIOL6 I 24 e Open PROGLETS DAT with WordPad Some of the lines in this file need to be made active Le un remarked by deleting the leading remarks character from the line This makes these lines active instructions and configures Science to operate these OPD and CTD sensors via their proglet programs Modify the lines as shown in example below proglets dat it it This file specifies the configuration of a Science computer in a Webb Research Glider it CTD41CP Sea bird CTD SBE 41 Continuous Profile Unit Seabird CID OES Persistor Hardware Pin 1 Power CTRL Pin 27 CTD5 it Pin 2 TX OUT J7pin25 UART4 RXC 3 Pin 3 MODE Pin 26 CTD6 Mote Brev Buster it 8 Save Proglets dat 9 Save and delete the Motelog1 txt file Return the flash card to the Science card socket 25 10 For G2 glider configured OPDs see appendix J Remove the 2 sample port covers 11 and replace with the test port covers with extension tubes Before inserting the ports into the water sample bottle with a water filled syringe fill the extenders with water to remove any air in the tubes Insert both tubes in a water sample bottle 12 13 14 15 16 17 18 19 Prepare Freewave serial com
10. Select Closed Reference Pump Off Turns CDOM reference pump off Sample Pump On Turns sample pump on Sample Pump Off Turns sample pump off Set Valve A Changes Valve to A port M i reverse sample pump runs sample pump in reverse mode Valcocal _ealibration for Valco port selector valve pos cal 38 Appendix G Setup Default Values set time to local No O set time to GMT Yes disc repeat rate E RENE Debug messageson e Debug messages off He CDOM ref Interval 9 CDOM refflushtime o CDOM ref Supply m 0 Mo CDOM ref on CDOM ref off CDOM Ref Pump speed jm CDOM Stroke Position Oo CdomRefPumpCal 10 39 Appendix H OPD error codes and the Status code The parameter Status is a 16 bit integer whose hexadecimal value is reported in the OPD status message Bit manipulation is used to encode the status of operational errors into the value of the integer Status The error types are pre assigned the following Hex and binary values Error Condition Hex Value Binary Equiv Each time that the OPD program tests for and finds one of the error conditions to be true it performs a bitwise OR into of the value of the error into the value of Status Example Status Status statPumpTimeOut This results in the bits of the binary value of Status each being encoded as either O or 1 in correlation with each of the error types as can be seen in the binary column of the error table
11. Setup amp control on your computer 36 Appendix F Opcodes nennen nenne 37 Appendix G Setup Default Values eeessseeeseeeeeeeeennnn 30 Appendix H OPD error codes and the Status code 40 Appendix I OPD CONFIG TXT descriptions 4 Appendix J G2 Glider OPD internal access 43 Section 1 General Information 1 1 General Description The Optical Phytoplankton Discriminator OPD is an electronic instrument that measures for the presence of algal organisms from their optical absorbance characteristics This is accomplished by pumping a water sample through a Liquid Waveguide Capillary Cell LWCC illuminating it with a light source and measuring the resulting light absorption spectra A single measurement cycle takes typically 5 minutes but may require as long as eight minutes The interval between cycles is programmable from continuous zero interval to several hours There are currently two models of the OPD instrument A low pressure model that 1s designed for shallow deployments and a high pressure model designed for AUV vertical profiler or towed deployments 100 meters maximum depth Typically also integrated into the AUV deployed model is a Sea Bird Electronics Inc CTD instrument which operates entirely independently of the OPD instrument After each cycle an OPD data report is logged internally and is sent to a h
12. ated and properly logged the comms between OPD and Science and between Science and Glider 3 2 Downloading Data Files from OPD 1 Downloading the key data files from OPD such as the Similarity Index values is typically done throughout the glider mission in the surface reports and then in more detail in the SBD data reports See a later section of this manual for configuration details of your glider files to enable this 2 OPD also logs all data in its Results folder on the flash card Uploading the data to your pc via flash card reader 1s the preferred data transfer method for the HP OPD unit Once uploaded and saved delete the contents of the OPD flash card Results folder before the next mission or test 3 3 Installine the OPD Leak Detection Cable l Delivered with the instrument is a new 2 conductor cable for connecting the OPD leak probe to the Glider s leak detection circuit Splicing this connection into your glider should be done before glider OPD deployment 2 Unplug connector J10 from leak on the glider control board 3 Cut the red and black leak sensor cable and splice the OPD blue cable wires into it Once done the two glider leak sensors as well as the 27 OPD leak sensor should all be connected to J10 and the glider s detection circuit Reconnect J10 Each time that you connect the aft umbilical cable from OPD to glider board you should next connect the OPD leak connector to its mate on the glider b
13. bbles and a low Similarity Index value of 0 2 or less for each cycle 16 6 When ready to stop or run another operation select stop from the sampling listbox The stop command will not stop a cycle immediately 1f you are running a cycle A stop requested message will appear 7 Select exit from the toolbar and wait for a message Log file closed followed by the command prompt C Power can then be turned off from the switch box 8 To exit the program select Close from the File menu 9 Remove the OPD flash card and inspect the log files in the Results folder as described in section 2 6 Ensure the debug txt file is not corrupt and that the 5 cycles just run were properly logged 2 7 Downloading Data Files In the high pressure model OPD it is much easier to access the Compact Flash memory card than in other OPD models as the card is accessible with the instrument fully assembled As download of data files requires removing the hull to supply power to OPD and then runs very slowly it s preferred that the user simply use a computer and CF card reader to open the Results folder and read copy and erase files by that means 2 8 Results Folder Files Saved in the Results folder of the OPD Compact Flash memory card are a variety of files 1 xxxxxxxx STT file Named automatically as SNyymmdd STT where SN is the units serial number yy is the year mm is the month and dd is the day This file contains all of the status messages of a sam
14. bug Show Swetem Files This selection opens the OPD program in Glider Mode Show Data Files Show Setup Files Show Species Files Show Archive Species Files Once the OPD program runs a message will appear on Sm m screen E Pressure C gt opd glider debug opd mooring debug uu E Voltage after Init 1s opa a t polled a 12 990506 volts ee wei Mcd fe Ok 10 14 09 13 13 29 High Pressure opd glider debug Ready opd glider debug nohast opd glider debug nohast sim SS E ZER en H EE The OPD instrument is now ready to run a cycle 3i cic 10 Click on BIOQMAY iyi TRO t080 939 4 f When selected the box turns blue OPD Mode Click for DOS II Now the OPD mode command list 1s populated on the left side of the screen If a cycle is running under the section Sampling select the STOP command 2 3 OPD Commands Note the OPD menu commands are executed immediately once single clicked on To avoid problems do not click on a command unless certain of its function In OPD mode the following basic commands appear in the left menu Command Definition Sampling Starts a run based on setup parameters Stops the currently running cycle After some delay the screen will read Stop Requested STOP will also bring the unit out of sleep mode Closes Log files and shuts down OPD Returns to PicoDOS The screen will say Log file closed EXIT will also bring the unit out of sleep mode Reports the status message after a cy
15. cle in polled mode This sets the number of sample cycles per run A value of 0 means an infinite number of cycles The value of 1 means one cycle will run the value of 2 means two cycles will run etc Number of minutes between cycle starts et time to local Sets time to local time Set time to GMT Sets time to Greenwich Mean Time Number of times the discriminate measurement is repeated in a cycle Disc repeat rate If 1 1s entered then it will do a total of 2 discriminate measurements per cycle Turns on Debug text reporting output to the console Designates the cycles at which a CDOM reference measurement is taken CDOM ref interval e g CDOM Ref Interval 9 would apply to cycle s 1 9 18 27 etc CDOM ref flush time Number of seconds that the CDOM reference pump and Sample pump will run in a cycle DOM ref supply Amount of CDOM ref fluid ml left in the CDOM ref supply bag CDOM reference on Turns CDOM ref part of measuring cycle on CDOM reference off Turns CDOM ref part of measuring cycle off SetDiscFlowTime The number of seconds of sample pump operation in the Discriminate portion of the cycle range 0 60 sec Reports the current sampling configuration settings By selecting Sampling Setup the user can view the current parameters set in the unit Sensors Report Reports serial number of unit firmware version bypass pressure value battery voltage sample syringe pump position depth leak status end of
16. cycle a value of 0 turns it off It should always be 1 unless troubleshooting DoCDOM 1 A value of 1 turns on the CDOM part of the cycle a value of 0 turns it off It should always be 1 unless troubleshooting DoDisc 1 A value of 1 turns on the Discriminate part of the cycle a value of 0 turns it off It should always be 1 unless troubleshooting GPSget 0 Reserved for future use where a GPS sensor is available Should always be 0 DiscFlowTime The number of seconds of sample pump operation in the Discriminate portion of the cycle range 0 60 sec Contact tech support before changing 42 Appendix J G2 Glider OPD internal access For the G2 glider the OPD sample ports have been moved to the forward hull ring and should not be 7 7 removed wem AES Instead remove forward science bay guard plate Take care to release the forward glider connectors from the plate before removing it e Ht 43 This allows access to the tubing and fittings including those connecting to the sample ports Fittings should only be tightened to firmly finger tight never using tools Unscrew the fitting marked V from its connection to the tee and the fitting marked P from its mating inline fitting Connect the adapter tubes provided to the P and V tubes that lead into the instrument These adapter tubes will be used to supply sample water to the instrument during bench and glider setup The othe
17. e NumberCycles 0 The number of measurement cycles to perform A value of 0 means an infinite number of cycles e CycleTimeMinutes 10 The number of minutes from one cycle start until the next cycle start e WaveSaveMin 350 The lower end of the wavelength range of saved raw spectra e WaveSaveMax 750 The upper end of the wavelength range of saved raw spectra e CdomRefFlushTime 30 The number of seconds the CdomRef pump runs during its portion of cycles designated by CdomRefRepeatInterval Also the number of seconds that the sample pump runs during the CDOM portion of the cycle while sample water is being filtered by the 0 22 micron filter e CdomRefRepeatInterval 9 The number of cycles between CdomRef reference measurements e DiscRepeat 1 Number of repeat discriminate samples A value of 1 results in a total of two pumped water samples of the discriminate unfiltered fluid where the second sample is less likely to be contaminated by either a precedent cdomref or water sample e FilterSize 47 The size of the Gaussian smoothing filter applied to the raw data e RunDepth 1 000000e 00 Not currently used e ShutDownDepth 5 000000e 01 Not currently used 4 FilterSigma 1 200000e 01 The width of the Gaussian smoothing filter applied to the raw data WriteTraces 1 Boolean value specifying whether or not to save raw spectra 1 Save 02 No Save DoCDOMkRef 1 A value of 1 turns on the CdomRef part of the
18. e narrow sharp edged end of the ring must face towards the yellow rubber ferrule This is very important since they play a key role in maintaining a proper water tight seal of the instrument and the AUV 6 Pull off the yellow ferrule then the stainless steel compression ring then the tubing to port nut and set aside Pull the free end of the orange Peek oi sample tube back through the hole in the ring being careful not to kink the tubing de Repeat these steps to remove the other sample port and tube 8 Use a 1 2 inch box wrench to unscrew the hex nuts that secure the aft ring 9 Locate the semi circular recesses on upper ring and use the hull separator tools supplied with your AUV by twisting back and forth to release the removable ring from the hull 10 Remove the hull from the CTD ring Velcro strap 2 2 Connections and Establishing Communications 1 Remove Velcro strap holding the CDOM reservoir bags 2 Place the OPD on its side with the syringe side up and leave the bags connected to the tubing i N M f vip lt Ya V pm ih A e at D ad 4 LS E a e y E d is d fis Ti t if 3 Locate the OPD power connector shown below and unplug the power cable from it Leaving the power switch turned OFF connect the power box and power supply to the OPD power connector Power box connector Mating Power connection 4 Find the RS 232 serial comm port near the compact flas
19. e order to Mote Marine Laboratory marked to attention of Phytoplankton Ecology Appendix C Configuring Glider files for operations with OPD Pre deployment of OPD To prepare for a real glider flight with OPD after all bench tests of OPD and Glider are done 1 be sure to change the file name of SIMUL SIM to SIMUL SAVE 2 Configure your SBD DAT and CONFIG SRF files as described below 3 Save a copy then delete the MOTELOGI TXT file from the science flash card A new log will be created in the real mission 4 Be sure that the file AUV BAT is in the root directory of the OPD flash card 5 Remember the 3 minute rule when exiting the glider program after the program tells you it s okay to remove power from the glider wait an additional 3 minutes before removing power to prevent corruption of the OPD files and program Appendix D Configuring glider for OPD parameter reports Below is a Sensor parameter listing for OPD t Mote Marine Lab Optical Phytoplankton Detector BreveBuster last modified ahails mote org 14 MAR 08 sensor uu motebb_on sec O d sensor sci_motebb_is_installed bool O installed on science sensor sci_motebb_sn nodim O d sensor sci_motebb status nodim O d sensor sci motebb volt nodim O d sensor sci motebb press nodim O sensor sci motebb cdomref nodim 0 d sensor sci motebb int time nodim O d 3 sensor sci_motebb_start_time timestamp sensor sci_motebb_stop_time tim
20. estamp sensor sci motebb absorb _a nodim Sensor sci motebb absorb b nodim sensor sci motebb corr0O nodim sensor sci motebb corrl nodim Sensor sci motebb corr2 nodim sensor sci motebb corr3 nodim sensor sci motebb corr4 nodim Sensor sci motebb corrb5 nodim sensor sci motebb corr nodim sensor sci motebb corr nodim sensor sci motebb corr8 nodim sensor sci motebb corr9 nodim sensor sci motebb corrl0 nodim Sensor sci motebb corri11 nodim sensor sci motebb logout nodim C SD 9 703 XX 9 3 X3 XX CO C 69 XX O H H H cH cH cH cH cH HEHEHE ce H che H E d The above parameters will be reported by OPD to Science then by Science to Glider at the end of each OPD measuring cycle At your discretion some of them may also then be reported to the user s Dockserver computer ashore by the glider via iridium or freewave radio by including them in your SBD reports change your SBDLIST DAT file and in surface reports change your CONFIG SRF file Be sure to run glider code version 6 34 or higher to ensure OPD compatibility In our proglet Mote has increased time delay to 90 sec in the routine MoteBB end to delay allowing Science to shut OPD down Now Science waits to get Log file closed from OPD If Science gets this message it sends sci motebb logout to glider then removes power from OPD If it does not get this message it removes power after 90 seconds has elapsed By adding this sc
21. h cards on the end of the instrument Disconnect and connect a DB 9 serial comms cable from your computer to the port attached to the plate This step replaces the Science board serial comms connection with a direct connection to your computer CF Card Science board 5 Connect extension tubing to the OPD sample port tubes Submerge the extenders in a water sample container Serial comm port connection Note If you have not already done so refer to Appendix E and install the OPD Setup and Control program on your computer 6 Open the OPD Setup and Control Program The setup page appears on screen ES OPD Setup and Control Version 4 1 0 0 SerialNumber Setup oH File Setup Control Data Display SOCOOL Windows Help UEC CMC SCENE Gronn 10 Communication Mode Serial Comm Port UDP Winsock Serial Comm Port 4 Comm Port Remote IP zi 19200 Remote Port 4131 LocalPort E We Set Working Folder C Program Files MOTE OPD Setup amp ControhDefaults Change Font Size 1 Number of time intervals after last P j data received betore itis assumed that all data is recen d Timer Interval for Monitoring Port i200 Transfer Packet Size 128 7 Choose the appropriate NISsETR Go ni ya corresponding to the computer port that you earlier connected to the OPD 10 8 Set the Baud Rate to 19200 Click on QUOI UY ROI emer enn The box will turn blue Comm is Open C
22. i motebb logout parameter to your glider surface reports you can monitor whether OPD is having its power removed prematurely Below are examples of both of those files located on the glider in its flash card at Gliderflash config 32 Root directory of Glider flash card File Edit View Favorites Tools Help O Back gt a yo Search lies Folders BR Folders A Mame Size Type Date Modified i Desktop app File Folder ON 12007 10 18 AM D E My Documents gt BN File Folder 12 19 2008 3 50 PM E dd My Computer config File Folder 12 19 2008 3 54 PM amp H 315 Floppy ci Loes File Folder 7 13 2012 11 05 AM E ze Local Disk fC C mafiles File Folder 12 19 2008 3 47 PM ES ia DVD RW Drive D missions File Falder 12 19 2008 3 47 PM E ve Removable Disk E C sENTLOGS File Folder 1O 22 2007 4 12 PM 3 w UNIT 055 I STATE File Falder FH 32012 11 01 AM LC app auteexec bat M5 D05 Batch File 112007 10 19 AM C BIN 9 config 9 Logs Directory of I config folder Se contig File Edit View Favorites Tools Help m sa T gt d P P Search d Ers Address Den SE Folders Mame Size Type Date Modified 3 Desktop al Autoexec mi GER MI File 12 19 2008 4 32 PM ES iE My Documents i config sci 1KB SCI File 12 10 2007 12 00 AM E 3 My Computer E CONFIG SRF 1KB Server Response File 12 19 2008 4 36 PM B H au Floppy A 1 dellag dat 1KB DATFile 12 10 2007 12 00 AM FE S Local Disk C highdens dat 1KB DAT F
23. ical properties In the similarity index SI analysis for K brevis identification the fourth derivative of the particulate absorption of an unknown sample is compared with the fourth derivative of the particulate absorption spectrum of a monospecific K brevis culture Results show that the SI correctly discerns K brevis from other members of natural mixed phytoplankton communities The reason for the success of this approach lies in the fact that K brevis displays unique absorption peaks at 444 and 469 nm owing to the presence of a particular photosynthetic pigment Fourth derivative analysis amplifies minor inflections in the absorption spectrum and so permits resolution and discrimination of this pigment In addition research has found that there is a linear relationship between K brevis biomass and SI magnitude permitting rapid determination of bloom magnitudes from the measurement In general SI readings above 0 6 on a scale from 0 0 to 1 0 indicate detection of a significant biomass of K brevis Research has now extended this measurement to numerous other plankton species The OPD instrument is provided with a library of Species Files capturing the absorption spectral fingerprints of K brevis and numerous other species For development of additional species parameter files please contact Mote Marine Laboratory s Phytoplankton Ecology Department Sim refers to an OPD program simulation mode It uses the parameters set up in the conf
24. iguration files to simulate measurement cycles and issue status messages but does not employ the pumps valves or sensors of the instrument This mode may be useful in testing the user s configuration of the instrument to be sure that it will perform on the schedule and in the modes desired once in a real operational mode PXE is a program file extension for PicoDOS eXEcutable files OPD PXE or OPD RUN is the executable program file firmware required for operation of the OPD instrument and must reside in the main root directory of its Compact Flash memory card Appendix B Replacement Parts he The hollow fiber membrane filter mounted on the edge of the OPD main chassis plate 1s specified as FILTER HOLLOW FIBER SPECTRUM LABS X12E 100 20N PKG OF 20 VWR PN 28170 590 As we buy these from VWR in qty you are welcome to buy these from Mote or to purchase directly from VWR or other supplier One spare filter 1s included in your spare parts kit 2 If you need to replace the screen mesh sample port filter elements that mount in the holders on the outside of the aft Science bay ring that is a custom part that you may purchase directly from Mote Two spare screen mesh filters are included in your spare parts kit 30 Part numbers and prices are listed below MOTE PART NUMBER DESCRIPTION UNITSPRICE 2038 FILTER SAMPLE PORT HIGH PRESSURE EA 48 00 144 yea HOLLOW FIBER SPECTRUM EA 2763 To order parts just send your purchas
25. ile 12 10 2007 12 00 AM ES i DVD RW Drive D t login ep ZER Exports Library File 12 10 2007 12 00 AM e Removable Disk E longterm dat ZER DAT File 12 10 2007 12 00 AM Sa LIMIT 055 1 mbdlist dat 1KB DAT File 12 10 2007 12 00 ON ICH app sbdlist dat 1KB DAT File 12 10 2007 12 00 AM CH BIM sensdata dat 44 KE DAT File 12 10 2007 12 00 AM mm SIMUL SIM 1KB SIMFile 11 20 2008 2 45 PM en LOGS zmext dat 2KB DAT File 12 10 2007 12 00 AM LH mafiles 33 SBDLIST DAT sample file j sbdlist dat WordPad PE File Edit View Insert Format Help DA Glo d 26 Jun O1 tcelHDinkumSoftware com reduced sensors for New Jersey O5 Sep O1 tcBDinkumSoftware com Added c wht lat lon m gps lat lon 14 Jul 03 fniDinkumSoftware com Added optional record interval secas If O or not present do it the old way 6 Sept OF ahailsfmote org removed water vx and vy added pitch m pitch c battpos m battpos l7 PROG AHAILS REMOVED TILDE AT END OF FILE 210CTOS AHAILSBMMOTE ORG ADDED sci motebh logout He H H E H H H CHE H PRESENT TIME M PRESENT SECS INTO MISSION M WATER VX H WATER VY H WATER DEPTH 15 H DEPTH 15 M LAT GU M LOW GU c WPT LON c WPT LAT H GPS LON H GPS LAT M WATER COND M WATER TEMP M WATER PRESSURE c PITCH H PITCH C BATTPOS M BATTPOS sci motebh sn O 15 sci motebh status sci motebh volt O 15 sci motebh press sci motebb cdomret sci motebhb int time sci motebh start time sci motebh sto
26. lick to Close Comm 10 In the tool bar click Control If the serial port opened successfully the cursor on the main part of the screen will be blinking 11 Before applying power to the instrument note that if it has been powered down for over 10 hours you may experience a delay of as long as 30 seconds after first applying power until you see a serial comms response the C prompt Please wait patiently with power applied while the power fail buffer capacitors are charged Turn power on to the instrument through the switchbox Warning once the instrument is powered on it should never have power removed unless the OPD program has logged off and you are returned to the C prompt 12 Below is the main header and C prompt in PicoDOS mode that appears in the text dialog center portion of the Control screen when the Persistor processor starts up Persistor CF2I5 SN 01944 PicoDOS V4 02r1 PBM V4 00 C 1998 2005 Persistor Instruments Inc www persistor com C gt T indicating that the OPD instrument is now up in PicoDOS Le DOS Mode and ready to run a program The program that you will run is named OPD PXE or OPD RUN PicoDOS executable programs OPD Setup and Con EIE vi File Setup Control Data Display In Dos Model choose the appropriate program for the type SCHOOL Help Windows rm m DOS Mode Click for OPD of unit involved When working with a High Pressure unit under the High Pressure submenu select opd glider de
27. ms then apply power to the Glider Glider battery power is preferred over a power supply for first operations after OPD has been idle As the glider operation begins Cntrl C to terminate the start sequence Turn off the bladder air pump Stop iridium calls Enter a local lat long near the first waypoint of your gotoL10 ma file Select zero_ocean_pressure Run a glider mission of your choice Consider a mission timeout setting of 15 minutes or so to get the glider to surface and report frequently Once Glider simulates flying and passes a depth of 2 meters on its first dive the proglet will command the OPD instrument to turn on and begin a cycle Subsequently OPD will continue to run measurement cycles at its configured Cycle Time whether ascending diving hovering or on the surface as long as its power supply is not interrupted If interrupted by Glider Science for SBD data file transfer 26 via iridium for example measurements will not resume until glider again dives below 2 meters 20 Allow the simulation to run until the Glider surfaces Verify in the glider surface report that OPD parameters less than 600 or so seconds old are reported 21 Stop operation exit gliderdos 22 Always wait 3 minutes before removing power or unplugging the aft umbilical cable to the glider 23 Remove the OPD and Science flash cards Verify OPD data has been logged successfully Verify that a new Motelogl txt file was cre
28. ng fluid and trapped air from two of the four smaller 2 5 mL syringes and out of the sample ports Check for any leaks around the syringes The pump will move to an end travel point and stop The purpose of doing this 1s to expel as many air bubbles from the sample syringes as possible If a bubble 1s later pumped into the optical waveguide it will reflect nearly all of the light and disrupt the measurement It is sometimes helpful 14 to incline the instrument just before pumping to encourage air bubbles to rise to the tubing fitting end of the syringes Repeat select Reverse Sample Pump The port selector valve will toggle and the syringe pump will move the syringe plungers in the opposite direction pushing fluid and trapped air from the other two sample syringes Repeat as many times necessary to remove the air 2 6 Testing and Operating the Instrument 1 To test the instrument run several measurement cycles Select the command AUV if this is in your command menu Otherwise type in the command AUV in the command box above the left menu selections then press enter This will test for the presence of the AUV BAT file in the OPD flash card root directory and if found will execute the command string OPD GLIDER NOHOST DEBUG If this does not occur replace the AUV BAT file 2 Set cycle time to zero numbers of cycles to 5 and set CDOMreference to On as described in section 2 3 11 Once the configuration is set the in
29. nkton will have been removed by the filter When running a CDOM Ref part of a cycle a similar message will appear while a sample of the reference fluid from the reservoir is measured for comparison to the water sample values Discriminate Pixel 1094 48687 Pixel 703 440nm 30097 Pixel 1095 51542 Pixel 703 440nm 32185 In the Discriminate part of the cycle the raw unfiltered water sample is measured In the case above with Disc repeat 1 two discriminate measurements of the same sample water are made Below is the final report message from the instrument at the end of the cycle The parameter descriptions of parts of the Status Message given in parenthesis are not part of the actual final report SerialNumber 27 BatteryVoltage 12 085 BypassPressure 2 343 Internal filter transmembrane pressure psi Status 200 Error Status code see Appendix H IntegrationTime 602 integration Time msec CDOMRefLeft 291 5 CDOM Ref remaining ml CycleStartTime 1297376558 Timestamps CycleStopTime 1297376624 AbsorbanceA 0 000 Absorbance slope AbsorbanceB 0 000 Absorbance intercept Corro 05 15 Species model used amp Similarity Index Please refer to the Glossary Appendix A for more details on Similarity Index and other aspects of the OPD operation 5 The instrument should run 5 complete measuring cycles with no sleep between logging a report message at the end of each Verify no leaks no sample syringe bu
30. nt with the CTD probe on the port side facing aft CTD probe 2 Connect ONLY the aft umbilical cable to the glider control board DO NOT CONNECT THE FORWARD UMBILICAL CABLE WHEN WORKING WITH THE GLIDER OPEN ON THE BENCH This will protect the ballast pump from being moved and damaged while not under vacuum 22 The entire system Glider Science and OPD has three main boards and flash cards associated with them The Glider has one in its aft end which has the function of running the glider operations Inside the OPD there are 2 flash cards both labeled The OPD card for the CPU which runs the instrument and the Science card for the CPU which integrates the Glider and OPD functions CF Card Science board 3 Locate the Glider flash card and remove from board Insert into PC flash card reader on the computer 4 Below is an example of the root directory of the glider flash card Note the file SIMUL X XX where X XX 1s either SIM or SAV Rename it to SIMUL SIM Wr config File Edit View Favorites Tools Help pack Ki d P Search E Folders Ei Folders x Mame Size Type Date Modified Desktop 9 Autoexec mi GER MI File 12 19 2008 4 32 PM My Documents i config sci 1 KB SCI File 12 10 2007 12 00 AM ES d My Computer CONFIG SRF 1 KB Server Response File 12 19 2008 4 36 PM JA 316 Floppy 4 3 dellag dat 1KB DAT File 12 10 2007 12 00 AM Se Local Disk C highdens det 1 KB DAT File 12 10 2007 12 00 AM id DVD RW
31. oard 28 Section 4 Appendices Appendix A Glossary l 10 11 Adjust int egration time is an instrument program sequence that appears near the beginning of each cycle It is best when integration time is low 60 msec or less indicating a clean well coupled optical path from the light source through the LWCC to the spectrometer Steadily rising values over time indicates progressive fouling of the LWCC Erratic values indicate entrained air bubbles or debris BSOP is an acronym for Bottom Stationed Ocean profiler a vehicle designed and developed by the University of South Florida s USF Center for Ocean Technology BSOP is an autonomous freely drifting vertically profiling vehicle designed for applications on the continental shelf By parking on the bottom between vertical water column profile depth excursions BSOP maintains its geographic station under typical continental shelf conditions BSOP carries sensors collects stores and transmits data via a bi directional satellite link Mote has supplied and USF has deployed a high pressure OPD instrument configured as one of the sensors of BSOP CDOM refers to Colored Dissolved Organic Matter In the context of this OPD manual we refer to the CDOM measurement part of the cycle where the water sample is filtered so that CDOM will remain but particles such as phytoplankton are removed by a filter The optical measurements of CDOM are then used to mathematically remove its
32. ost computer or any telemetry system that supports serial data communications In the typical case of AUV deployment in a Webb Research Corp electric glider the host computer 1s the science bay Persistor computer The OPD is designed once started to operate autonomously NOHOST mode or under the step by step control of a host HOSTED mode There are a number of user settable parameters that are used by the program to set the operating mode sample the water acquire spectral data analyze the data calculate a phytoplankton similarity index and to log and report the results This manual will guide the user for basic functions of the instrument 1 2 Specifications Mechanical Weight in air 13 kg Diameter 21 cm excluding CTD probe Length 30 cm Depth Limit 70 meters maximum Electrical Voltage 12v DC Current 600 mA average while sampling Current 50 mA while in sleep mode between cycles 1 3 Contents of Shipping Case OPD instrument Spare parts kit Power supply wall plug Power switch box with cable Sample port flush fittings 2 OPD HP User Manual Section 2 Operations and Maintenance PREPARATION FOR DEPLOYMENT Prior to deploying the OPD two preparatory tasks are required e The Optical Phytoplankton Detector is shipped with 2 internal fluid reservoirs the CDOM Reference water supply bag and CDOM Reference waste fluid bag The supply reservoir needs to be filled and the waste reservoir emptied prior to deplo
33. p time sci motebb absorb a sci motebb absorb b sci motebh corr sci motebh logout CO OO OO DO oO For Help press F1 34 E Sample CONFIG SRF file El CONFIG SRF WordPad Sel File Edit View Insert Format Help Cah Glo d amp e D IN for nia 1 vu og m battery sci motebb corr sci motebb status sci motebb logout I vacu m leakdetect voltage For Help press F1 35 Appendix E Installing OPD Setup amp control on your computer On the web go to http coolgate mote org socool downloads Click on OPD Setup amp Control OPD Installer txt will have instructions on how to download to your computer 1 Unzip OPD Setup amp Control to a local folder 2 Run setup exe 3 Run regscom bat Default location c Program Files Phytoplankton Ecology OPD SetupControl 4 Launch OPDSetupControl exe 36 Appendix F Opcodes tart top Exit tatus cycles to do cycle time et time to Local et time to GMT Disc repeat rate lt discrepeat gt amp I DN un Messages on debugon Messages Off debugoff dom ref interval lt cdomrefrepeatrate gt amp I Cdom ref flush time cdomrefflushtime amp I CDOM ref Supply mL lt cdomrefmliterleft gt amp I DOM reference on cdomrefon CDOM reference off cdomrefoff DiscFlowTime opcode 99 Reports Report HP OPD Commands il SEI Shute Closed Deuteriumon Turns Deuterium light only on M i Turns all lights off urns al igh of
34. pling event Status messages are described in section 2 4 2 XXXXXxxx LOG Named as yymmddss LOG where yy is the year mm is the month dd is the day and ss is the second The log files contain a mixture of character strings and spectrometer readings The program OPD Analysis is available from Mote for viewing and interpreting log files 4 DEBUG TXT is a text file record of every step of the measurement cycles commands received error messages status messages etc logged and timestamped as the instrument operates The file is best viewed with the Windows WORDPAD program Example of data displayed in a DEBUG TXT file SN 17 cycle 1 of 0 cycles with cycletime 0 17 117289707 20252252 Voltage before starting cycle 1 is 12 546347 volts Adjust integration time 93 ms Pixel 1095 59103 Pixel 703 440nm 37196 84 ms Pixel 1095 54417 Pixel 703 440nm 34266 Valid integration time 84 ms Dark Pixel 399 2455 Pixel 703 440nm 2400 CDOM Pixel 1095 54265 Pixel 703 440nm 34337 Discriminate Pixel 1094 48687 Pixel 703 440nm 30097 Pixel 1095 51542 Pixel 703 440nm 32185 SerialNumber 27 BatteryVoltage 12 085 BypassPressure 2 343 Status 200 IntegrationTime 62 CDOMRefLeft 291 5 CycleStartiime 1297370358 CycleStopTime 1297376624 AbsorbanceA 0 000 AbsorbanceB 0 000 corro 0 15 4 current log amp tmp log These are active back up copies of the primary log files 2 9 Filter
35. r instructions of this manual apply to both the G1 and G2 configured OPD instruments 44
36. strument is ready to run a cycle Ensure the sample fluid supply 1s ready the sample port tubes still immersed and the Cdomref bags are still connected 3 Click on Start to begin the measurement cycle 4 As the cycle s are in progress the data displayed on the screen describes the progress of the run Verify that the sample syringe pump operates and moves the syringes through several strokes interrupted by optical measurements Below is an annotated example of a typical cycle session SN 19 cycle 1 of 0 cycles with cycletime 0 12720707 104557232 Voltage before starting cycle 1 is 12 546347 volts First part of message informs of instrument Serial number cycle number that will run and total number of cycles cycle time date and time and battery voltage instrument currently has Adjust integration time 95 ne Integration time is the Length of time in msec the spectrometer collects pixels to make the peak value 54000 59000 Pixel 1095 59103 Pixel 705 440nm 37196 84 ms 15 Pixel 1095 54417 Pixel 703 440nm 34266 Valid integration time 84 ms Dark Pixel 399 2455 Pixel 703 440nm 2400 Dark is a Spectrometer measurement run without light Pixel values will be low compared to other parts of the cycle CDOM Pixel 1095 54265 Pixel 703 440nm 34337 In the CDOM measurement part of the cycle the sample is filtered so that CDOM will remain in the water but particles euch as phytopla
37. yment e Water samples are collected in a series of syringes driven by a syringe pump Air that has entered the sample lines during shipping or storage needs to be removed before operation To accomplish these tasks the hull must be removed for access 2 1 OPD Internal Access l Place the instrument vertically on a surface with the CTD ring facing down Rest it on supports or blocks to avoid damage to cables A 9 64 Allen wrench is needed to remove the sample ports Note See appendix J if your OPD is configured for a TRW Webb Research G2 model glider and do not remove the sample ports Remove both screws from each sample port Remove the transparent cover copper mask and screen mesh filter element leaving the black plastic filter base on the instrument The filter base is attached to tubing Separate the filter base from the instrument by carefully prying it away from the ring while drawing a short length of orange tubing thru the ring opening 4 Using pliers grip the end of the tubing to port nut above the o ring and turn the sample port base counterclockwise to unscrew it from the fitting Remove base 5 The yellow tubing ferrule and orange Peek tube are now exposed Using a flat head screwdriver lightly separate the stainless steel compression ring from the ferrule Note When removing the metal compression ring note its orientation The flattened end of the ring must face towards the nut th
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