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SeaFET pH Sensor

1. After the USB Serial Driver Setup dialog appears a Windows Security dialog requests confirmation before proceeding to install the driver Would you like to install this device software Name Satlantic LP Ports COM amp LPT lt a Publisher Satlantic LP V Always trust software from Satlantic LP r You should only install driver software from publishers you trust How can decide which device software is safe to install Check the Always trust software from Satlantic LP option Press the Install button to confirm trust in software provided by Satlantic and to complete the USB Serial driver installation Installing Satlantic USB Serial Driver on Windows XP CAUTION The SeaFETCom program must not be running when completing the Satlantic USB Serial Driver installation on Windows XP If SeaFETCom is running while installing the USB Serial driver on Windows XP the driver installation will fail After the driver installation steps are completed and before SeaFETCom is run the driver must be activated by connecting the SeaFET to one of the computer s available USB ports 27 118 SeaFET Manual Software Connect the SeaFET to a USB port then select the No not this time and Install the software automatically Recommended options on the following Found New Hardware Wizard dialogs Found New Hardware Wizard Welcome to the Found New Hardware Wizard Windows will search for current and
2. Connection Status Connected Available Disk Space 3 550 MBytes 94 SeaFET Clock Time 05 Sep 2014 18 03 28 UTC Power Supply Voltage 11 837 Main Battery Voltage Isolated Battery Voltage 5 9 101 118 SeaFET Manual Maintenance Calibration SeaFET calibrated at the Satlantic facility using a single point calibration at 0 5m depth An estimate of the pH reported on the total scale referred to herein as the standard value associated with a water sample drawn in the vicinity of the sensor is obtained through an implementation of the spectrophotometric pH determination technique developed by Byrne et al 1988 Clayton and Byrne 1993 Cell potentials recorded by the SeaFET coincident in time with water sampling are used together with the standard value of pH to compute a set of coefficients Calibration coefficients are stored on SeaFET Coefficients are in used conjunction with an on board temperature measurement and the user selectable salinity constant see Processing Settings to calculate pH from the cell voltage potentials of the FET The calculated pH value is sent within each data frame generated by SeaFET Calibration coefficients are written to the header section of every data file logged by SeaFET When reprocessing previously logged data SeaFETCom retrieves the coefficients from the header records of each file to be reprocessed To ensure the highest level of accuracy of both on board
3. Upload Cancel Default Help 52 118 SeaFET Manual Settings External Pump Settings SeaFET Settings General Telemetry Processing External Pump cro Pump Data 7 Enable External Pump Pumping Duration 30 sec Sampling Delay 30 sec Sampling Event 40s Pump Off esata tie O 5 10 15 20 25 30 35 40 45 50 55 60 65 70 Note The active sampling time is based on the SeaFET s currently selected operational mode and its sampling settings Cancel Defaut Hep Enable External Pump setting enables or disables use of an external pump by the SeaFET Pumping Duration is the time in seconds that the external pump is on Note When the external pump is setup to be on during sampling it will remain on until sampling has completed Sampling Delay is the time in seconds between when an acquisition event starts and when data sampling starts By setting the sampling delay greater than the pump duration SeaFET will pump wait and then sample with the pump off The Sampling Event graph the has two horizontal bars e Pump to show when the external pump is turned on and off for each sampling event Data to show when data sampling starts and stops for each sampling event Note A hint is displayed when the mouse cursor is placed over each section of a bar 53 118 SeaFET Manual Settings CTD Settings SeaFET S
4. Response Timeout 5 sec File Listing Timeout 30 gt sec Automatic Serial Connection Default Data Directory C Users glenn Documents Browse Prompt at startup Data Directory Preferences 39 118 SeaFET Manual Software To set software preferences for file storage location on the host computer select the General tab and refer to the Data Directory preferences Default Data Directory indicates the file system folder to which SeaFETCom will write all data log files and event files Press the Browse button to select an alternate directory path or type paste a path directly in the input box Prompt at startup indicated whether or not SeaFETCom will prompt you to review and possibly change the default data directory each time the application starts This option is useful if there are multiple SeaFET s being used on one computer Display Preferences To review and modify software display preferences select the General tab and refer to these input fields Sensor Value Decimal Places shows the number of decimal places used to display sensor values in the Real Time Display window To adjust the displayed precision type a new number or press the up down arrow buttons Use UTC Time indicates whether time values displayed by SeaFET com are shown in Coordinated Universal Time UTC or the local time zone of the host computer Click the checkbox to toggle between UTC or the computer s Time Zone for all time values d
5. e Do not attempt to upgrade SeaFET firmware unless directed to do so by Satlantic e If the procedure is interrupted the instrument is left without a working firmware 103 118 SeaFET Manual Troubleshooting Troubleshooting Invalid Frames in data Within any data logging application there is a possibility that corrupt data values can get into a frame For each corrupt frame the user should see a message such as Lost Bytes in the Application tab of the output panel In addition to this the SeaFETCom Error Event panel should be displayed in SeaFETCom SeaFETCom will display this frame corruption then ignore these corrupt data points and continue No Connection to SeaFET If SeaFETCom is unable to establish a connection to SeaFET attempt to connect to SeaFET using a terminal emulation program such as TerraTerm or HyperTerm SeaFET uses the following serial connection settings Data Bits Stop Bits Flow Control Baud rate can be changed by the user but is initially set to 57600 when shipped If a connection cannot be established then please contact Satlantic support support satlantic com SeaFETCom Message Logs All activity that occurs with SeaFETCom is logged to disk in an application log file The location of these log files is shown in the Message Logging Settings dialog that can be opened from the Edit menu Although the contents of the log are somewhat cryptic and mainly for use by Satlantic personnel
6. Installation Press Finish button to exit the Found New Hardware Wizard Found New Hardware Wizard 7x Completing the Found New a Hardware Wizard SS The wizard has finished installing the software for 3 SeaFET CDC Virtual COM Port pe Click Finish to close the wizard lt Back Cancel Installing SeaFETCom on Mac OS X Prerequisites for running SeaFETCom on Mac e Intel based Mac iMac MacBook or Mac Mini running OS X 10 7 or newer e Java SE 6 for OS X installed and updated e User account installing and using SeaFETCom must have administrative privilege 29 118 SeaFET Manual Software To install the software run the SeaFETCom self extracting pkg file found on your SeaFET product CD ROM or at http satlantic com seafetcom The installer is named in the form SeaFETCom lt version gt b lt build gt x86_64 pkg e g SeaFETCom 1 1 2 b87 x86_64 pkg The installer program steps through the install process The default option can be selected at each confirmation step Please ensure that the default option of Install for all users on this computer is retained as the install location destination If this option is changed to Install for me only or Install on a specific disk the USB serial driver configuration will prevent successful connection to SeaFET 30 118 SeaFET Manual Software Navigating SeaFETCom SeaFETCom provides a Menu for navigating all available actions and a flex
7. Run SeaFETCom and connect to SeaFET see Connecting to SeaFET 2 Select Sensor gt Set Clock from the main menu 3 Press the Sync Time button to set SeaFET instrument clock to equal the time on the computer clock CAUTION The SeaFET clock is always set to Coordinated Universal Time UTC regardless of whether the times in the Set Clock dialog are configured to display local time or UTC The Use UTC Time option in the SeaFETCom Preferences dialog determines whether times are displayed in UTC a Set Clock Instrument Time 13 Mar 2012 19 17 47 UTC Computer Time 13 Mar 2012 19 17 48 UTC Sync Time Cancel Help 55 118 SeaFET Manual Settings Summary Report Before a deployment or when it is important to record the complete state of the SeaFET instrument it is recommended to create a Summary Report To do this 1 Connect to SeaFET and enter setup mode 2 Select Sensor gt Summary Report from the main menu to show the Summary Report dialog 3 Type your name in the Operator Name field 4 Type comments in the Summary Report Comments field 5 Check the View Report option to view the generated report in your default PDF viewer 6 Press the Browse button to change the output folder named in the Directory field Summary Report Operator Name John Smith Summary Report Comments File Name Report 30 03 2012 1113 pdf E View Report Directory C Data SeaFETCom Bro
8. SAT for a Satlantic instrument followed by three characters identifying the frame type The last four characters are the instrument serial number Example for serial number 0001 SATPHB0001 Sample Date UTC in format YYYYDDD Sample Time UTC in format DECIMALHOUR FET INT calculated pH in total scale STATUS AS6 Status word a 16 bit hexadecimal formatted bitmask indicating system status CHECK SUM Al 1 3 The sum of all bytes up to an including the checksum value should be 0 109 118 SeaFET Manual Data Formats Reference TERMINATOR This field marks the end of the data frame with a carriage return line feed pair hexadecimal 0x0D and Ox0A The maximum number of characters in a Short ASCII frame is 101 CTD Data Frame Format NOTE Units reported will depend on the appropriate configuration of the CTD output format Refer to the CTD user manual for instructions on how to configure the output units HEADER AS 10 The frame header or synchronization string starts with SAT for a Satlantic instrument followed by three characters identifying the frame type The last four characters are the instrument serial number Example for serial number 0001 SATPHCO0001 Conductivity S m Date and Time YYYY MM DDThh mm ss ex 2014 03 24T13 03 55 TERMINATOR This field marks the end of the data frame with a carriage return line feed pair hexadecimal 0x0D and 0x0A The maximum number of characters in a CTD
9. after processing Displaying Processing Results Results from SeaFET data processing are displayed within a custom graph that displays the original pH temperature and salinity values and also the processed pH values In addition the temperature and salinity values used during processing are also displayed Note that nothing is displayed for the CTD temperature and salinity values when they are not available as would be the case if there was no attached CTD when the data was collected Processed pH Data Viewer 38 ENES w E ETEEN Processed pH Time Series Processed pH INT Processed pH EXT E 9 fi iginal pH INT E Q 3 J pH iginal pH EXT E F Q 3 stor Temp 9 3 g 3 o 3 Bo El 2 fe Q m ssing Temp El in o FET Salinity y 8 a 4 o Salinity B Processing Salinity Date amp Time psu 00 00 00 000 Time Original pH INT Original pH EXT Processed pH INT Processed pH EXT Temp CTD Temp Processing Temp lt gt Onboard Salinity CTD Salinity Processing Salinity 89 118 SeaFET Manual Recovery and Processing By clicking on the graph a crosshair at a particular point in time can be displayed It is placed on the graph at the closest time with corresponding data The data values from all plots corresponding to the crosshair point are displayed in the boxes along the left h
10. c Salinity Practical PSU 6 Press the Start Process button to create a cnv file 87 118 SeaFET Manual Recovery and Processing The data section following the header meta data in the resulting cnv file should look something like this 388682568 10 8326 34 8974 0 000e 00 388682574 10 8547 34 8950 0 000e 00 388682580 10 8517 34 9032 0 000e 00 388682586 10 8670 34 9007 0 000e 00 388682592 10 8889 34 8926 0 000e 00 To minimize additional steps on subsequent conversion operations use the Program setup file panel to save your SeaFET specific conversion configuration as a new psa file A sample psa file for converting SBE37 data to SeaFET format is available at http satlantic com DatCnv SEB37 SeaFETCom 1 0 0 psa Time Stamp Options Select the Offset option to specify a positive or negative time offset to apply to the external temperature salinity data This can be used to compensate for clock drift or time zone differences between CTD data and SeaFET data Temperature Options Select one of the Temperature Options to indicate the source of temperature data e Temperature from External File The temperature values used for SeaFET data processing are taken from the external File e Temperature from SeaFET Data Frames The temperature values used for SeaFET data processing are those from the internal thermistor taken from the SeaFET data frames e CTD Temperature from SeaFET Data Frames The temperature values used
11. data frames which are otherwise normally discarded 43 118 SeaFET Manual Settings Settings Topics in this chapter include e SeaFET Settings e Telemetry Settings e Processing Settings e Setting the Clock e Summary Report 44 118 SeaFET Manual Settings SeaFET Settings Operational Mode Settings SeaFETCom can be used to configure the following operating modes Continuous Periodic and Polled Polled and Periodic operating modes are most convenient for power limited applications e g when SeaFET is powered by the internal battery and or an auxiliary external battery Polled mode is used when SeaFET is integrated with an external master controller capable of requesting data Periodic mode is ideal for autonomous operation e In Continuous mode SeaFET makes measurements continuously as specified by the current sampling settings such as sampling average size and frame type SeaFET does not sleep or stop measuring until it is commanded to return Setup mode or power is exhausted e In Periodic mode SeaFET autonomously makes a set of measurements as specified by the sampling parameters such as average size burst size and frame type at a specified sampling interval In between sampling events SeaFET goes to sleep In Polled mode SeaFET remains in low power sleep state until woken by an external command to make a measurement After the measurement is complete and data sent logged SeaFET returns to low
12. frame is 91 110 118 SeaFET Manual Using a Terminal Emulator Using a Terminal Emulator The following is an example of how to deploy a SeaFET Ocean pH Sensor using a terminal emulator 10 11 Remove the dummy plug from the SeaFET connector and connect the test cable Secure the locking sleeve Connect the data end of the test cable to a computer If using the RS 232 interface connect the test cable DB9 connector to a serial port or to a serial to USB adapter to a USB port If using the USB interface a Install the USB driver bundled with the SeaFETCom installer first time only b Connect the USB male connector to a USB port and wait for the host to recognize the sensor c Anew COM port virtual should become available NOTE COM number varies host to host Using a terminal emulator such as HyperTerm or TeraTerm open a connection at 57600 bps 8 bits no parity 1 stop bit If using the RS 232 interface connect the test cable power jacks to a 12V DC power supply and switch it on If connecting through the USB interface power will be drawn from the host USB bus Observe SeaFET output in terminal emulator NOTE If connected through the USB virtual COM or if the internal batteries were previously connected you may not see output until breaking into the command console Step 6 Enter repeatedly to break into commanded mode You should see the command prompt SeaFET gt Set system clock
13. power sleep and does not sample again until another command is received The General settings tab will change to reflect the applicable settings for the selected operational mode 45 118 SeaFET Manual Settings SeaF ET Settings General Telemetry Processing External Pump CTD Operational Mode Continuous X Sample Averaging Number of Samples in Average 1 Number of Frames in Burst 30 Optional Sample Date Range Enable Sampling Window Begin sampling on this date 2000 01 01 UTC Stop sampling on this date 2038 01 01 UTC Internal Device Logging Logging Level Maximum Log File Size 1024 gt KB Deployment Characteristics Estimated Frame Rate 10 00 frames sec Estimated Battery Life 11 days Estimated Total Samples 9180000 Estimated Effective Interval minutes Estimated Sample Duration minutes Continuous Mode Settings Select Select Cancel Default Help Most of the following settings are used when SeaFET is in Continuous operational mode In this mode a stream of data frames is output continuously until main power is disconnected or SeaFET receives a command to enter Setup mode Sample Averaging Number of Samples in Average Specifies the number of pH measurements to average for the output data frame Raw data is averaged before calculating the pH values In some environments increasing this value can reduce noise and produce more
14. select the sensors to display in the Time Series view i Configure Graph a Time Axis Range Limit Temperature Supply Voltage ox Lena ee _concet_ te _ 73 118 SeaFET Manual Integration with an External Pump Logging Real Time Data SeaFET has ample internal storage to log months or even years of sensor data which is ideal for autonomous deployment For tethered operation such as a profiling cast or pre deployment test SeaFETCom can be commanded to log a copy of the sensor data as it is transmitted in real time To log SeaFET data in real time 1 Connect to SeaFET 2 In SeaFET Settings dialog set operating mode to Continuous 3 Press Start button on the Dashboard 4 Select View gt Data Logging on the SeaFETCom main menu 5 Press Start Log button to begin logging acquired SeaFET data The Data Logging window allows you to create a separate log that is a subset of the current acquisition When an active acquisition is underway press the Start Log button to begin logging data to a local file Once enough data has been logged simply press the Stop Log button to finish logging The Auto Log Duration and Repeat Auto Log after Interval values hh mm ss are used to log data to multiple data files when the Start Log button is pressed By enabling the Auto Log Duration option data logging will automatically stop after the specified duration time
15. to diagnose problems within the application it will often provide clues to errors that exist within the application Each line in the log represents an event that occurs within the application Below is a short explanation of the format of a logged message to assist the user in trying to self diagnose problems that may occur A logged message has the following format lt Date Time gt lt Module gt lt Code gt lt Message gt lt optional stack trace gt Date Time Displays the date and time when the message was logged Module Displays the module that initiated the log message i e Internal Core or GUI 104 118 SeaFET Manual Troubleshooting Code Internal code i e ISC 1100 ERR describing the module internal error number and severity Severity is either INF info WRN warning or ERR error Message A text based representation of the event Stack Trace Optionally occurs when unexpected errors happen to show the state of the application when the error occurred Here is an example that shows an error that occurred when trying to connect to a SeaFET 2008 03 80 10 25 21 UTC java io FileNotFoundException at java io FileInputStream at java io FileInputStream seafet seafet seafet at com satlantic ph at com satlantic ph at com satlantic ph at java lang Thread SeaFETCom ISC 6804 ERR Calculate file identity failed C Program Files Satlantic SeaFETCom 1 0 0 CURRENT CAL
16. 000 CSV 2014 03 27 00 00 06 127219459 csv bat Date se Te 14086000 CSV 2014 03 27 12 34 06 60893411 csv A0000546 CSV 2013 01 30 14 25 31 421 csv 14084000 CSV 2014 03 26 00 00 00 44695978 csv A0000005 CSV A0000002 CSV A0000004 CSV 2014 01 14 14 43 02 5380 csv A0000003 CSV 2014 01 14 14 42 12 4108 csv elect All Delete Refresh Select All Delete a The File Manager dialog shows two tab buttons each of which provides access to a category of files e Data Files sensor data files e Log Files errors warnings and diagnostics files To download files to your computer e Press the Browse button in the Local File System pane to select the local folder that will receive the downloaded files In the Instrument File System panel select the files to be downloaded from the SeaFET e Press the lt left arrow button between the panels to transfer the selected files e If a download is taking too long the Cancel button can be pressed to cancel the download e Monitor the transfer progress bar Do not exit the program or disconnect SeaFET until the progress bar reports 100 To free internal SeaFET storage space by removing files e Ensure that the files to be deleted have been completely and successfully downloaded to the computer before proceeding Deleted data files cannot be recovered e In the Instrument File System panel select the files to be deleted 81 118 SeaFET Manual Recovery and Processing e Press the D
17. 15 Lost Bytes 153 Frame Errors 0 Error Details Time Series Graph The time series graph shows a history or all pH and temperature readings reported by the SeaFET since start of data acquisition 71 118 SeaFET Manual Integration with an External Pump Ej Output se Time Series SeaFETOD06 se GHW Q Zoom In OY Zoom Out f Auto Range v Time Axis Range Axis Select Sensors Configure Time Series 12 5 10 0 ae 75 5 0 25 12 5 10 0 ue 78 5 0 25 24 600 24 575 o 24 550 24 525 16 21 00 16 21 30 16 22 00 16 22 30 16 23 00 16 23 30 16 24 00 16 24 30 16 25 00 16 25 30 16 26 00 16 26 30 16 27 00 16 27 30 16 28 00 Time UTC pH Internal Reference pH External Reference Temperature Zooming and Panning on the Time Series Graph Zooming in and out of the Time Series Graph can be accomplished in several ways The first is by the use of the zoom buttons at the top left of the Time Series Graph The Zoom In and Zoom Out buttons will zoom the plots around the date center point The Auto Range button resets the graph so that the whole data range is visible The check boxes control which axes these three buttons work on If both are checked zooming is enabled on both axis Otherwise zooming only occurs along the checked axis If neither is checked the zoom buttons are disabled Note that clicking on one of the plots with the mouse c
18. 2 6027 4 669 10 523 0 05975991 0 85879952 1 13056064 11 326 114 0 5 4 882 9 602 6 106 5 903 100 100 0 95693927 0x0000 7 lt CR gt lt LF gt Short ASCII frame example SATPHB0001 2014083 13 0932646 7 80829 7 78879 20 5221 20 5038 32 6027 4 669 10 523 0x0000 234 lt CR gt lt LF gt The following tables define fields for each frame The integer component of the Format column specifies the fixed size or variable size range of the described field SeaFET Full ASCII Data Frame Format HEADER AS 10 The frame header or synchronization string starts with SAT for a Satlantic instrument followed by three characters identifying the frame type The last four characters are the instrument serial number Example for serial number 0001 SATPHA0001 DATE Sample Date UTC in format YYYYDDD 107 118 SeaFET Manual Data Formats Reference Sample Time UTC in format DECIMALHOUR eo p peee O C E STATUS Status word a 16 bit hexadecimal formatted bitmask indicating system status 108 118 SeaFET Manual Data Formats Reference The sum of all bytes up to an including the checksum value should be 0 CHECK SUM Al 1 3 TERMINATOR AS 2 This field marks the end of the data frame with a carriage return line feed pair hexadecimal 0x0D and Ox0A The maximum number of characters in a Full ASCII frame is 197 SeaFET Short ASCII Data Frame Format HEADER AS 10 The frame header or synchronization string starts with
19. Com Overview The Satlantic SeaFET Ocean pH Sensor comes complete with SeaFETCom an interactive graphic software application Connect the SeaFET to your computer via the supplied USB programming cable to enjoy these SeaFETCom features e Review and modify SeaFET operational settings Schedule SeaFET data collection activity Manage and retrieve logged SeaFET data View SeaFET data in real time e Reprocess SeaFET data and graph results SeaFETCom provides the tools necessary to configure and operate your SeaFET ph sensor for any deployment scenario Manage on board data storage processing and collection modes Set up real time data streaming via USB or RS 232 Capture and plot data in real time for pre deployment checks or interactive profiling casts Re process logged pH data using ancillary temperature and salinity inputs for improved accuracy SeakETCom 120 22 Sra SeaFETCom Sens ate View Window tF Zorkd Qe Search rh SeaFETCom Dashboard Window a Time Series SeaET0393 2 Kee Correcion eck AISI Amn Zemou Aroren V Tine Asis F Range ass sehctsensrs SE certigae s Time Series Connection Stabs Connected Available Disk Space 3 765 MBytes 100 z D SeaFET Settings SeaFET Cock Tims 26 May 2014 14 43 04 UTC E Ed Generel Telematry Procassing Extemai Pump CTO Power Supply Woltage 12 433 a Operations Moda Corkins Main Battery Vokage 0 8 TD Co
20. DO NOT ALLOW THE WET CAP STORAGE SOLUTION TO FREEZE DURING SHIPPING OR STORAGE THIS WILL DAMAGE THE DURAFET AND VOID THE WARRANTY Precautions Avoid touching sensing elements Avoid allowing the ISFET internal reference electrode to dry out Avoid exposing the electrodes to hydrofluoric acid Avoid exposing the sensor to high purity water e g Milli Q Super Q in many cases clean tap water is preferred over distilled water Accumulation of bubbles on electrode sensing surfaces is to be avoided The solution in many cases involves proper instrument orientation Diligence in choosing a deployment site that does not place the sensor in direct exposure to natural sources of bubbles is also recommended Do not leave SeaFET in direct sunlight when not being used Extreme heat 35 C or greater can cause damage Cleaning of Electrode Surfaces 1 Place the instrument on a bench or table such that the end cap bearing the electrodes and bulkhead connector are facing up Remove instrument wet cap or foul guards as appropriate The electrodes may be placed under warm flowing tap water in order to remove particulates For oily deposits household detergents such as Joy or Windex may be used Laboratory detergents such as Sparkleen may be used The recommended cleaning procedure for any mineral deposits consists of rinsing the electrode in dilute acid e g hydrochloric acid rinse thoroughly following acid cleaning with distill
21. Data Recovery e SeaFET Sensor Data e Data Processing 77 118 SeaFET Manual Recovery and Processing SeaFET Recovery Instrument Handling Consult the Safety and Hazards section to familiarize yourself with safe handling procedures and potential hazards Particular attention should be paid to the warning describing the safety procedure when removing the instrument end cap Handle the instrument carefully ensuring that the sensing head is protected at all times by means of either the foul guard or the wet cap Upon initial recovery of the instrument and following an inspection of the sensing elements install the instrument wet cap if it was not already in place for a special application deployment The wet cap installation procedure is documented in the Preventative Maintenance section of this manual Ensure that the wet cap is filled with sterilized artificial seawater Data Retrieval Data files logged internally on a SeaFET can be listed and retrieved using either e SeaFETCom File Manager or e SeaFET USB Mass Storage For more information see Data Recovery Shut down Stand by Depending on the anticipated post recovery instrument down time it may be advantageous to fully power off SeaFET to preserve its internal battery s charge Note however that the sensing element requires a continuous current flow to provide stable readings Once shut down the instrument may take up to 24 hours to warm up and provide stable
22. Deployment Scenarios 58 E External Interfaces 18 External Pump Settings 53 F Firmware Upgrade 103 l Installing SeaFETCom 26 Instrument Drawings 17 L Logging Real Time Data 74 M Maintenance 92 Major Components 14 Message Logging 42 N Navigating SeaFETCom 31 0 On The Cover 23 Overview 9 P Power Supplies 20 Preventative Maintenance 95 Principle of Operation 11 Processing Settings 52 Q Quick Start 7 R Real Time Data Acquisition 69 Recovery and Processing 77 References 117 S SeaFETCom Dashboard 35 SeaFETCom Overview 25 SeaFETCom Preferences 39 SeaFET Deployment 67 SeaFET Recovery 78 SeaFET Sensor Data 83 SeaFET Settings 45 Settings 44 Setting the Clock 55 Software 24 Specifications 22 Storage and Shipping 93 Summary Report 56 T Telemetry Settings 50 Troubleshooting 104 U Using a Terminal Emulator 111 118 118
23. FET and processed accordingly Electrical Integration The relevant signals for CTD integration are documented in the External Interfaces section At a minimum V along with CTD TXD data transmission from SeaFET to CTD and CTD_RXD data reception from 61 118 SeaFET Manual Integration with a SBE 37 CTD Optional Feature CTD should be connected to the CTD ground reception and transmission lines respectively If the SeaFET is to provide power to the CTD then the CTD V line should be connected to the CTD power input line SeaFET Configuration To enable CTD interoperation refer to the CTD Settings section in this manual Interoperation with the SBE 37 is available in all three operational modes polled periodic and continuous However for a stand alone or logger controlled deployment the periodic and polled mode should be selected respectively When operating alongside with the SBE 37 the SeaFET will periodically poll for CTD data and use it for pH calculation Since pumping needs to take place in the SBE 37 it usually takes in the order of 40 seconds to start outputting data that the SeaFET can use for pH calculation For this reason frames will take a while to appear at the telemetry port after the sampling event is started Also note that power consumption will be increased due to the extended time the SeaFET needs to be active See the Battery Endurance section in this manual for an example of how the CTD impacts powe
24. FET for more information If the SeaFET internal batteries are not already activated the Internal Battery Voltage Too Low warning dialog is shown Activate the internal batteries by connecting an external power supply and then pressing the Retry button The main battery and isolated battery voltage readings will be update Press the SeaFET Settings button on the SeaFETCom dashboard to open the SeaFET Settings dialog Press F1 key for help on any selected setting Select the Continuous operational mode Press the OK button to apply changes Press the Start button on the SeaFETCom dashboard SeaFET will simultaneously transmit data to SeaFETCom and log it internally SeaFETCom will display graphic plots of SeaFET sensor data as they are received in real time Select the Stop button on the SeaFETCom dashboard to stop data acquisition 7 118 SeaFET Manual Quick Start 11 Open SeaFET Settings dialog and select Polled mode to put SeaFET in low power standby Note that SeaFET can operate immediately after power is applied but it does require up to 24 hours on standby power to achieve optimal sensor stability 8 118 SeaFET Manual Overview Overview This chapter provides an overview of SeaFET how the sensor works and physical and electrical specifications Topics in this chapter include e About SeaFET Principle of Operation e Major Components Instrument Drawings External Interfaces e Power Supp
25. FO v Display Dialog for Error Level Messages Daily Log Files Rolling Log Files Maximum Number 10 Maximum Size 256 KB Lost Bytes Log File Enable Logging Lost Bytes Logging Level allows you to select the sensitivity of the SeaFETCom application logs The following logging levels can be selected All logging levels are cumulative i e INFO level also logs WARN and ERROR e TRACE Most verbose level of logging It generates very large log files It should only be used by Satlantic support staff for troubleshooting e DEBUG Moderately verbose logging of debug messages It is mainly used by Satlantic support staff for troubleshooting e INFO Typical log level for normal operation It logs all high level operations e WARN Only logs warnings that occur in the application It does not record INFO log messages e ERROR Only logs errors Errors typically require investigation and intervention Display Dialog for Error level Messages shows a pop up alert whenever an ERROR or SEVERE message is logged This ensures that application errors requiring investigation and intervention are not missed Daily Log Files causes a new message log file to be created each day 42 118 SeaFET Manual Software Rolling Log Files retains only a Maximum Number of message log files each no larger than Maximum Size Enable Logging Lost Bytes can asist in problem diagnosis by logging extraneous bytes or incomplete
26. G Power Supply Return Signal Ground USB V USB 5V Power MCBH8M Male Face View os eer ee peee Indicator LED The SeaFET is equipped with a bi color indicator LED The LED will flash with different patterns and colors to indicate a variety of situations Flashing pattern Meaning Green short blink 6 Starting continuous sampling mode Sampling Green long blink Starting periodic mode Green long and short blink Starting polled mode Red long blink pose Deactivating internal batteries Note that the SeaFET will periodically flash the indicator green when acquiring data This feature will work for the first 24 hours after the SeaFET is applied power either from activating the internal batteries or from connecting a live power supply to VIN After 24 hours the sampling indication will cease in order to preserve power Notice that if the instrument is set in periodic or polled mode the sampling indication will only be shown during the sampling event as opposed to all the time Magnetic Switch 18 118 SeaFET Manual Overview The SeaFET features a magnetic sensor that allows the user to activate or deactivate the internal batteries simply by approaching a magnet to the switch target Note that the magnetic switch will only operate if the internal batteries are installed Activating the internal batteries Remember that the internal batteries need to be activated prior deployment To activa
27. SEA BIRD SCIENTIFIC SeaFET pH Sensor SATLANTIC SeaFET Firmware Version 3 6 0 and later SeaFETCom Software Version 1 2 4 Document No SAT DN 00590 1 2 4 51 Date 2015 01 08 03 36 Satlantic LP 3481 North Marginal Road Halifax Nova Scotia Canada B3K 5X8 Tel 1 902 492 4780 info satlantic com www satlantic com Copyright 2015 Satlantic LP 3481 North Marginal Road Halifax Nova Scotia B3K 5X8 Canada All rights reserved Table of Contents Cautions and Hazards Quick Start Overview About SeaFET 10 Principle of Operation 11 Major Components 14 Instrument Drawings 17 External Interfaces 18 Power Supplies 20 Specifications 22 On The Cover 23 Software 24 SeaFETCom Overview 25 Installing SeaFETCom 26 Navigating SeaFETCom 31 SeaFETCom Dashboard 35 Connecting to SeaFET 37 SeaFETCom Preferences 39 Message Logging 42 Settings 44 SeaFET Settings 45 Telemetry Settings 50 Processing Settings 52 External Pump Settings 53 CTD Settings 54 Setting the Clock 55 Summary Report 56 Deployment 57 Deployment Scenarios 58 Integration with a SBE 37 CTD 61 Integration with an External Pump 63 Battery Endurance 64 SeaFET Deployment 67 Real Time Data Acquisition 69 Acquisition Display 71 Logging Real Time Data 74 Data Logging Headers 75 Acquisition Monitor 76 Recovery and Processing 77 SeaFET Recovery 77 Data Recovery 80 SeaFET Sensor Data 83 Data Processing 84 Main
28. SeaFET gt set clock yyyy mm dd hh mm ss Configure Operational Mode i For continuous operation SeaFET gt set opermode continuous ii Or for periodic scheduled operation including the sampling interval number of samples per event SeaFET gt set opermode periodic SeaFET gt set perdival 1h Ex one event each hour SeaFET gt set brstsize 5 Ex 5 samples per event Configure the averaging size per sample SeaFET gt set navg 10 Ex average 10 measurements per sample Ensure that the internal batteries are activated SeaFET gt batton Start sampling SeaFET gt exit 111 118 SeaFET Manual Using a Terminal Emulator 12 13 14 15 If using the USB interface eject unmount the SeaFET from your OS and unplug the USB cable Connect a power cable or re install the dummy plug for self powered deployment Remove wet cap and install anti fouling guard Deploy SeaFET 112 118 SeaFET Manual Command Reference Command Reference SeaFET can be configured and controlled via its serial command line interface To access the SeaFET command line interface via a terminal emulation program please refer to Using a Terminal Emulator Commands set lt setting gt lt value gt get lt setting gt list pkg data log send pkg data log lt file gt receive pkg data log lt file gt delete pkg data log lt file gt chksum pkg d
29. The system cannot f open Native Method lt init gt FileInputStream java 106 Ancillary calculateIdentity Ancillary java 205 ui actions simple SerialConnectAction attachedToPort SerialConnectActio ancillary AttemptConnectPort run AttemptConnectPort java 155 run Thread java 619 Such stack trace messages can help Satlantic support engineers diagnose errors When reporting an error to Satlantic please have the following information on hand e The version of SeaFETCom you are using see SeaFETCom About dialog e The version of firmware and serial number of the SeaFET you are using see SeaFETCom Dashboard e The following files o SeaFET logged raw data file o SeaFETCom message log file 105 118 SeaFET Manual Contact Satlantic Contact Satlantic If you have any questions comments or concerns about your SeaFET please contact us Satlantic 3481 North Marginal Road Halifax Nova Scotia Canada B3K 5X8 Tel 1 902 492 4780 Fax 1 902 492 4781 Email Technical Support support satlantic com General Inquiries info satlantic com Web http www satlantic com Business Hours Satlantic is normally open for business between the hours of 9 00 AM and 5 00 PM Atlantic Time Atlantic Time is one hour ahead of the Eastern Time Daylight saving time is in effect from 2 00 AM on the second Sunday in March through 2 00 AM on the first Sunday in November Atlantic Standard Time AST is UTC 4 Atlantic Dayl
30. U AWK and Microsoft Windows PowerShell are very effective The most ubiquitous data manipulation application is Microsoft Excel Follow these basic steps to use Excel to convert data to the format required by SeaFETCom e Import data into Excel e Convert date time to a single YYYY MM DD hh mmi ss text field e Remove all columns except date time temperature and salinity e Re order columns to match the lt date time gt lt temperature gt lt salinity gt ordering required e Save as a comma delimited text file Sea Bird CTD Converted File In addition to the generic CSV format described above SeaFETCom can also ingest temperature and salinity measurements from a file in a specific cnv converted format as generated by the SBE Data Processing software application provided by Sea Bird Electronics http seabird com for their line of CTD conductivity temperature depth sensor packages To convert your Sea Bird CTD data to a compatible format for SeaFETCom 1 Copy your hex and xmlicon CTD files to the SBE Data Processing input directory example C Program Files Sea Bird SBEDataProcessing Win32 2 From the SBE Data Processing main menu select Run gt Data Conversion 3 In the File Setup tab select your hex and xmlcon input files 4 In the Data Setup tab press Select Output Variables 5 In the Select Output Variables dialog add these fields in order a Time Instrument seconds b Temperature ITS 90 degC
31. air of pliers Be sure to stand behind the end cap Be extremely careful as if the instrument is pressurized the end cap may be forced out of the housing with extreme force and at high velocity This work must be performed in a well ventilated area NO BATTERY IS INTRINSICALLY SAFE Use care when connecting power supply cables to the instrument A shorted power supply or battery can output maximum current potentially harming persons equipment or perhaps a fuse In preparation for transport or shipping install the dummy plug with locking sleeve on the instrument connector to prevent accidental shorting of the terminals Handle electrical terminations carefully as they are not designed to withstand strain Disconnect the cables from the bulkhead connector by pulling on the connector heads and not the cables Do not twist or wiggle the connector while pulling as this will damage the connector pins Do not use petroleum based lubricants on connectors Connectors should be free of dirt and lightly lubricated before mating We recommend applying a thin film of DC 111 silicone grease made by Dow Corning on the male pins prior to connection While probing with a voltmeter take care not to short the probes Shorts can damage equipment create safety 5 118 SeaFET Manual Cautions And Hazards hazards and blow embedded fuses e Do not leave batteries inside the instrument if it is not going to be used for an extended p
32. al SeaFET system logs e DEBUG High level log logging detailed mainly used by support for troubleshooting problems e INFO Typical log level for deployment contains logs for all high level operations e WARN Only logs warnings that occur in system suitable for long deployments e ERROR Only logs errors typically errors require investigation and user intervention All log levels are cumulative i e INFO level also includes WARN and ERROR messages Maximum Log File Size The maximum size of each system log file internally logged by the SeaFET since there is at most two system log files the max size allocated for internal logging is 2x Maximum Log Size 48 118 SeaFET Manual Settings Deployment Characteristics The Deployment Characteristics panel displays estimated values that are helpful when configuring SeaFET for deployment Estimated Frame Rate Displays the estimated frame rate of the instrument The frame rate is dependent on the Number of Samples in Average setting Estimated Battery Life Displays the estimated battery life in days for the instrument The battery life is dependent on the nominal battery capacity and the number of sampling events and the duration of each event The number of sampling events is dependent on the Operational Mode setting ie Continuous or Periodic For Periodic Operational Mode the number of sampling events is the Estimated Effective Interval and the duration of each event i
33. and side of the graph Clicking on the arrow buttons will move the crosshair in the corresponding direction The values of the boxes are updated accordingly Each plot has a checkbox associated with it Clicking on the check box toggles the display of the associated plot on and off The checkbox colour corresponds to that used in the associated plot The SeaFET Data Processing Results The SeaFET Data Processing results are saved in the output directory location within time stamped data files that contain log file headers with creation and processing information The format of each frame of data saved in the file is described in the table below Header AS 10 The frame header or synchronization string starts with SAT fora Satlantic instrument followed by three characters identifying the frame as SeaFET Processed PHP The last four characters are the instrument serial number Ex SATPHP0001 Date Al The date from the raw data file with the format YYYYDDD i e 2012046 The time from the raw data file in decimal hours i e 16 4261 The Internal pH calculated by SeaFETCom External pH Temperature Processed Internal pH Processing Temperature The temperature C used for processing SeaFET raw data frame Processing Salinity The salinity PSU used for processing the SeaFET raw data frame Processed AF The External pH calculated by SeaFETCom External pH 90 118 SeaFET Manual Recovery and Processing Proce
34. arge de rating 0 95 factor is applied to cover pre deployment storage time and deployment duration To estimate the deployment duration D 3 58 35s 9x 10 x 0 1 s 900 s 0 0528 Tdm 14 710 mAh 0 0528 x 30mA 9290 h 387 days Tdi 14 710 mAh 1 0 0528 x 1 1 mA 14118 h 588 days The estimated deployment duration will then be 387 days provided that the CTD has enough battery power to operate during such period of time Please refer to the CTD documentation for instructions on how to estimate its battery endurance 66 118 SeaFET Manual Integration with an External Pump SeaFET Deployment 1 Use SeaFETCom to configure the SeaFET Operational Mode and other desired settings 2 If using the USB interface eject or unmount the SeaFET drive from your OS then unplug the USB cable 3 Ensure the internal batteries are installed and activated NOTE Once the batteries are activated the instrument will commence its sampling routine An indicator LED will signal the start of the sampling program Refer to the External interfaces section for details on the indicator LED blinking patterns 4 If applicable connect a power or data logger cable Or re install the dummy plug if the instrument is to operate in stand alone mode 5 Remove the wet cap Install the anti fouling guard see procedures below 6 Deploy SeaFET WARNING Internal batteries MUST be installed and activated before deployment Failure
35. ase the latter is not available and establishing connection to SeaFETCom is not an option 14 118 SeaFET Manual Overview Foul Guard Controller Electronics Plastic Housing Batteries Battery End Cap Slot Battery End Cap Power Data Connector Handle Magnetic Switch Target Indicator LED Relief Plug 15 118 SeaFET Manual Overview The sensor end cap is opposite the battery end cap The sensor end cap exposes two sensors the ISFET sensor and the external reference electrode Both sensors must be covered by a seawater filled wet cap for shipping and storage The wet cap doubles as a flow cell with inflow and outflow attachments for connection to a pumped sample supply For fully immersed operation the wet cap is replaced by a perforated copper anti foul guard ISFET Sensor External Reference Wet Cap Flow Cell Electrode Copper Nickel Tube 16 118 SeaFET Manual Overview Instrument Drawings 94 48in 11 4em 20 00in 50 8cm 17 118 SeaFET Manual Overview External Interfaces Bulkhead Connector A single underwater connectable SubConn MCBHE8M electrical connector on the sensor end cap combines power and data communications interfaces to the SeaFET Power and data communications functions assigned to each of the eight pins are identified in the table below Description External DC Power Supply 6 18 Vdc V S
36. ata log lt file gt chbaud dmesg lt dump_size_in_bytes gt freset force all Change various settings See below tables for relevant settings Ex SeaFET gt set baudrate 115200 Read various settings and parameters See below tables for relevant settings parameters Ex SeaFET gt get clock List directory contents Ex SeaFET gt list data Transfer a sensor file to the host via XMODEM Ex SeaFET gt send data CO000001 csv Transfer a host file to the sensor via XMODEM Ex SeaFET gt receive pkg SEAFO009 zip Erase a file Asterisk erases all files in a directory Ex SeaFET gt delete data C0000001 csv Get a file checksum Ex SeaFET gt chksum pkg SEAF0009 zip Refresh telemetry baudrate immediately Baudrate will otherwise be refreshed upon rebooting the sensor Dump latest system messages Resets the sensor settings to factory defaults The all argument also resets the file counters NOTE Ensure there are no data log files in the system when using this switch 113 118 SeaFET Manual Command Reference Reboots the sensor NOTE Will reset USB connections ctdterm Start a CTD Terminal The SeaFET will act as a gateway to the slave CTD syncctd Force a time synchronization between the SeaFET and the CTD The CTD will get the SeaFET time battoff Disconnect the internal batteries NOTE To be used for storage or shipping to preserve batteries The internal batteries m
37. ce is allowed for system log files and other uses Estimate based on single file containing FULL ASCII frames Sample Rate 10 Hz max Internal Batteries 12 x 1 5V Alkaline D Cells External Supply 6 18 VDC Power Consumption Operating 340 400mW from the external supply or main battery pack 10uA from the isolated battery pack Standby 70uA from the external power supply or main battery pack 1 1mA from the isolated battery pack Communication RS 232 9 6 115 2 kbps USB 12Mbit s 5 4 kg 0 1 kg in water including internal batteries 22 118 SeaFET Manual Overview On The Cover The SeaFETCom icon also on the cover of this manual is a representation of a hydronium ion The presence of hydronium ions relative to hydroxide determines pH Water molecules auto dissociate into hydronium and hydroxide ions in the following equilibrium 2H20 is in equilibrium with OH H3s0 In pure water the number of hydroxide ions is equal to the number of hydronium ions 23 118 SeaFET Manual Software Software SeaFET comes compete with SeaFETCom a graphical software application for configuring and controlling SeaFET and for managing and processing data Topics in this chapter include e SeaFETCom Overview Installing SeaFETCom Navigating SeaFETCom e SeaFETCom Dashboard e Connecting to SeaFET e SeaFETCom Preferences e Message Logging 24 118 SeaFET Manual Software SeaFET
38. consistent measurements Note that the data frame rate is affected by sample averaging Number of Frames in Burst 46 118 SeaFET Manual Settings Specifies the number of data frames in a burst of data frames Note This setting is only used when SeaFET is in either Periodic or Polled operational mode Optional Sample Date Range Note These settings are only used when SeaFET is in either Continuous or Periodic operational mode Enable Sampling Window When this option is enabled the sampling window date range settings are used to restrict when sampling can occur Begin sampling on this date The date after which sampling can occur This date is for the UTC time zone and the display format is YYYY MM DD Stop sampling on this date The date after which sampling can not occur This date is for the UTC time zone and the display format is YYYY MM DD Polled Mode Settings The above settings are also applicable for Polled mode except for the Optional Sample Data Range settings Periodic Mode Settings The Periodic Mode Settings will appear in the General settings tab when Periodic operational mode is selected SeaFET Settings Ea General Telemetry Processing External Pump CTD Operational Mode Periodic Mode Settings Sample Interval 1 hr x Offset 0 sec The following settings are applicable only to the Periodic mode Sample Interval 47 118 SeaFET Manual Settings This setting
39. controls the timing between collection events For example the value 1 hr indicates that an acquisition event occurs once every hour Offset An offset in seconds is applied before each sample interval thus delaying the start of each collection event Understanding the Periodic Mode The periodic mode equally divides the 24 hour day into intervals defined by the Sample Interval For instance 6 hr will result in a total of four intervals each six hours long starting at 00 00 hr 06 00 hr 12 00 hr and 18 00 hr To delay the sample interval start time the offset can be used An offset of 300 seconds 5 minutes will change our example interval start times to 00 05 hr 06 05 hr 12 05 hr and 18 05 hr Within those intervals there is an acquisition duration defined by either the number of frames or the duration per acquisition period Each of these acquisition periods should be less than the sample interval This can not strictly be enforced for frame based samples because the rate is affected by the properties of the measurement sample and system settings Internal Device Logging SeaFET maintains a system log file that can be downloaded using the SeaFETCom file transfer dialog The SeaFET log file MESSAGES LOG will increase in size until it hits the maximum log size Once this occurs it will be backed up to a second log file overwriting the previous backup file MSG_OLD LOG Logging Level Select the verbosity of the intern
40. cting installer program found on your SeaFET product CD ROM or at http satlantic com seafetcom The installer is named in the form SeaFETCom lt version gt b lt build gt x86 exe e g SeaFETCom 1 1 2 b147 x86 exe The installer program steps through the install process The default option can be selected at each confirmation step Installing Satlantic USB Serial Driver on Windows 7 or Vista The last step in the installer is to install the Satlantic USB Serial Driver SeaFETCom requires this to be run at least once in order to connect to a SeaFET via a USB virtual serial port On subsequent installs or upgrades this step can be skipped WARNING SeaFET must not be attached to a USB port when the Satlantic USB Serial Driver is being installed If it is the USB Serial driver will not function correctly resulting in communication failures The installation of the Satlantic USB Serial driver causes the following dialog to be displayed 26 118 SeaFET Manual Software Execute C Program Files x86 Satlantic Satlantic USB Serial Driver 1 0 dpinst64 exe lm s en Output folder C Program Files x86 Satiantic Satlantic USB Serial Driver 1 0 Extract dpinst32 exe 100 Extract dpinst64 exe 100 Extract Satlantic_CDC inf 100 Created uninstaller C Program Files x86 Satlantic Satlantic USB Serial Driver 1 0 Execute C Program Files x86 Satlantic Satlantic USB Serial Driver 1 0 dpinst64 e
41. ction to SeaFET Advanced sub menu lists some less commonly used sensor actions Command Terminal opens a input dialog to send firmware commands directly to the connected SeaFET See Command Reference for more information Data Log Headers open the Data Log Headers dialog to define ancillary information to be written the top of sensor data files logged in real time by SeaFETCom Upload Firmware File update or restore the operating firmware on the connected SeaFET Upload Coefficients allows the user to upload a calibration coefficients file to the SeaFET See Calibration for more information Disconnect for Storage allows the user to disconnect the internal batteries of the SeaFET to prepare it for storage or shipping See Storage and Shipping for more information Data menu lists actions for reprocessing logged SeaFET sensor data SeaFET Data Processing opens the Data Processing panel in the dashboard area View menu Graphs Time Series Graph shows the Time Series Graph for viewing acquired sensor data in real time Processed pH Graph shows the Processed pH Graph for viewing re processed results Output menu actions show a specific tab in the Output Window Setup Console shows the Setup Console in the Output Window 32 118 SeaFET Manual Software Acquisition Console shows the Application Console in the Output Window Post Processed Console shows the Post Processed Console in the Output Window Application Cons
42. de Indicated by a green background 35 118 SeaFET Manual Software Connection Status indicates if the software is Connected or Disconnected to the local serial communications port The Connected status does not necessarily imply connection to SeaFET itself The following fields display status information retrieved from the SeaFET to which SeaFETCom is connected These fields are empty if there is no connection to SeaFET Available Disk Space displays the number of gigabytes and overall percentage space remaining on the internal storage device of the SeaFET to which SeaFETCom is connected The percentage of space available on the device will always be less than 100 due to system files such as firmware and configuration SeaFET Clock Time shows the time reported by SeaFET s internal clock The internal clock is always set to the Coordinated Universal Time UTC time zone The dashboard will display this clock time in the local time zone of the host computer when the Use UTC Time option in the SeaFETCom Preferences is not selected Power Supply Voltage displays either the internal battery or external power supply voltage which ever is greater reported by the connected SeaFET Main Battery Voltage displays the voltage of the Main battery back as reported by the connected SeaFET Isolated Battery Voltage displays the voltage of the Isolated battery back as reported by the connected SeaFET Deployable Status displays if the con
43. e advantages of the ISFET include robustness stability and precision that make it suitable for ocean pH measurement at low pressure T R Martz J G Connery K S Johnson Testing the Honeywell Durafet for seawater pH applications Limnology and Oceanography Methods 8 172 184 2010 SeaFET has two potentiometric cells the internal cell and the external cell Both cells are immersed in the sensed medium The names internal and external refer to the arrangement of the reference electrodes in each cell The internal cell consists of the ISFET as the working electrode and an Ag AgCl electrode bathed in a saturated KCI solution gel as the internal reference electrode The internal reference electrode is bathed in a saturated KCI solution gel so that the chloride concentration that the electrode sees remains relatively constant Note that Ag AgCl electrodes exhibit primary sensitivity to chloride ions The solution is in a compartment within the instrument the connection to the sensed medium is through an annular frit which encircles the post So again internal refers to the fact that the reference electrode is somewhat isolated from the sensed medium its electrical potential is proportional to the concentration of chloride of the KCI gel which is not expected to vary considerably Note however that the liquid junction at the seawater KCL interface generates an electrical potential because ions diffuse through the fri
44. eaFET in real time 1 FULL_ASCII Configures SeaFET to transmit full ASCII data frames over the USB and RS 232 interfaces when acquiring data See Data Formats Reference for a description of the long ASCII frame FULL_ASCII is the default SeaFET data transmission setting 2 SHORT_ASCII Configures SeaFET to transmit short ASCII data frames through its USB and RS 232 interfaces when acquiring data See Data Formats Reference for a description of the short ASCII frame 3 NONE Turns off real time SeaFET data transmission SeaFET will not transmit data through through its USB or RS 232 interfaces when acquiring data 50 118 SeaFET Manual Settings br gt Transmit Diagnostic Messages causes SeaFET to transmit diagnostic messages on the USB and RS 232 interfaces The Logging Level option in the SeaFET Settings dialog sets the level of information transmitted in the diagnostic messages Use this option only when diagnosing a problem It must be turned off during normal operation Instrument Logging Frame Format sets the data format to be recorded internally by SeaFET 1 FULL_ASCII Configures SeaFET to record full ASCII data frames on internal storage See Data Formats Reference for a description of the long ASCII frame FULL_ASCII is the default SeaFET data transmission setting 2 SHORT_ASCII Configures SeaFET to record short ASCII data frames on internal storage See Data Formats Reference for a description of the short ASCII f
45. ed and isolated source of power to keep the sensing element conditioned Note that re conditioning of the sensing element due to loss of power could take up to 24 hours hence the need for keeping it permanently powered during deployment This power source also needs to be isolated from the system ground in order to achieve the desired noise performance As explained before this uninterrupted and isolated power is derived from the internal batteries For this reason batteries must be installed and activated before deployment The internal batteries can be activated from the SeaFETCom dashboard or by using the magnetic switch WARNING Internal batteries MUST be installed and activated before deployment Failure to do so will result in unusable data Batteries can be activated from the SeaFETCom dashboard or by using the magnetic switch External power input VIN Power can also be supplied through an external input VIN 6 18V When the voltage level in this input is at or above 9V the instrument will draw power from it hence preserving battery power Note that even if 20 118 SeaFET Manual Overview external power is applied throughout a deployment the instrument will still need the batteries in order to keep the sensing element powered during low power standby 21 118 SeaFET Manual Overview Specifications Data Storage Over 18 million samples Approximately 85 of storage is available for sensor data Remaining spa
46. ed water The sensing elements may be wiped gently with non linting tissues or cotton swaps without damage The external reference electrode may periodically be polished by rubbing the supplied polishing film over the electrode surface for 30 sec 95 118 SeaFET Manual Maintenance Battery Replacement The SeaFET battery compartment holds 12 alkaline D Cell batteries These batteries can be replaced when needed following the instructions below For this procedure you will need the following tools and accesories e 8 32 thumb screw e 5 32 hex driver e 1 4 socket driver e A flat head screw driver e 2x fresh desiccant packs or a resealable bag to temporarily preserve the ones in use e 12 x new D cells Step 1 Remove the vent plug Lay SeaFET on its side on a flat surface Ensure the sensing elements are protected by the wet cap or by the foul guard Thread 8 32 thumb screw into the center thread of the vent plug Pull on the thumb screw until it does not come out any further Pull the vent plug Step 2 Remove end cap screws Using a 5 32 hex driver or Allen key loosen and remove each of the three 10 32 x 3 8 screws from the battery end cap 96 118 SeaFET Manual Maintenance Step 3 Remove end cap Insert a flat head screwdriver into the end cap slot and use it to pry open the end cap until it can be grasped with your hand Once the cap has been pried outward enough to get a good g
47. elete button e When prompted confirm the delete operation 82 118 SeaFET Manual Recovery and Processing SeaFET Sensor Data SeaFET simultaneously streams and stores data frames Streamed and stored data frames can be of different formats That is SeaFET can be configured to stream short frames and store long frames or vice versa The internally logged data can be retrieved through USB mass storage or by using the Transfer Files function of SeaFETCom See Data Formats Reference for a full description of both long and short frames Data File Syntax When using the USB Mass storage interface data files resulting from the sampling operation are stored in the DATA directory Three data file generation rules are determined by the Log File Creation Method e By File Size Data is stored in a single file until it size reaches a pre specified limit datfsize setting These files are named incrementally from CO000000 csv to C9999999 csv e By Sampling Event A new file is generated for each sampling event These files are named incrementally from AO0000000 csv to A9999999 csv e Daily The sensor generates one file per day These files are named as yydddnnn csv where yy is the year and ddd is the day of the year and nnn is a sequence number NOTE A file is generated in a given day only if a sample event occurs Changes to any settings that will effect data processi
48. eriod of time e Do not mix used and new cells nor different chemistries when replacing the instrument batteries 6 118 SeaFET Manual Quick Start Quick Start 10 CAUTION Read this manual thoroughly before operating your SeaFET At a minimum before attempting the quick start instructions below you must understand all warnings and cautions cited in sections Safety and Hazards and Maintenance Execute the SeaFETCom installation program as described in the Installing SeaFETCom section of this manual From the Windows menu bar select Start gt Programs gt SeaFETCom gt SeaFETCom to start SeaFETCom Remove the dummy plug from the SeaFET eight pin connector Connect the supplied USB or RS 232 programming cable to SeaFET Secure the locking sleeve If an RS 232 cable is being used connect the DB9 end to the host computer serial port and the power leads to a live power supply See the Specifications section for appropriate external power supply voltage levels If a USB programming cable is being used connect it to an available USB port on the host computer A new virtual serial port such as COM1 will appear in the Windows device manager list The indicator LED will blink a few times indicating power was applied to the instrument Press the Connect button on the SeaFETCom dashboard to open the Serial Connect dialog Select the SeaFET virtual com port example COM1 and press Connect See section Connecting to Sea
49. etting which defines the a number of frames to output The data frames will continue to be acquired periodically until the Acquisition Stop button is pressed Periodic Acquisition Ea fi The instrument s current clock time is 29 Mar 2012 20 47 53 UTC The next periodic acquisition start time is 29 Mar 2012 21 00 00 UTC Polled When the Acquisition Start button is pressed the Polled Mode dialog warns that SeaFET must be configured for either Continuous or Periodic Mode in order to acquire data from SeaFET using SeaFETCom Polled Mode x SeaFET is currently configured in Polled Mode Please change to Continuous or Periodic Mode in order to take a sample 70 118 SeaFET Manual Integration with an External Pump Acquisition Display SeaFETCom is set up to display data collected from SeaFET in both real time and graphical views All the data displays are described below Real Time Display When an acquisition starts the Real Time Display data view will appear on the bottom left area of the main application window The Real Time Display is continuously updated to show the most recent pH and temperature values reported by the SeaFET Real Time Display SeaFET0003 Select Sensors Name Value Units pH Internal Reference 7 9364 Temperature 20 7438 Bi 2 Acquisition Information Acquisition Statistics SeaFET0003 Time Stamp 11 Apr 2012 17 29 11 UTC Frames Read
50. ettings Sa General Telemetry Processing External Pump CTD Seabird 37 SMP ODO V Enable CTD V Power CTD Output CTD Frames Sampling Timeout 120 sec Sample Delay 30 sec Seabird 37 SMP ODO Settings These settings are used by the SeaFET to control an integrated Seabird 37 SMP ODO CTD Enable CTD setting enables or disables use of the CTD by the SeaFET Power CTD setting enables or disables supplying power to the CTD by the SeaFET Output CTD Frames setting enables or disables transmission of data frames from the CTD by the SeaFET Sampling Timeout is the maximum time seconds that the SeaFET will wait to receive a data frame requested from the CTD Sample Delay is the time seconds that the SeaFET delays ISFET parameters sampling pH ISFET T etc after a sampling event begins This feature can be used to allow for the measurements to stabilize after the CTD pumps a fresh volume of water and before the SeaFET starts data recording and streaming Note This setting is ignored in Continuous mode and when use of an External Pump is enabled 54 118 SeaFET Manual Settings Setting the Clock SeaFET has an internal clock SeaFET uses its internal clock to apply date time stamps to logged data and to schedule sensor activity The internal clock can drift over time The internal clock should be synchronized with a reliable time source To synchronize the SeaFET clock with a computer 1
51. for SeaFET data processing are those from an attached SeaBird CTD instrument taken from the SeaFET data frames Note that selecting this temperature source from a file that does not contain CTD temperature values will cause an error dialogue to open e Offset An offset applied to the temperature whether that from an extern file that from the SeaFET Data Frames or that from the CTD instrument used in processing Salinity Options e Salinity from External File The salinity values used for SeaFET data processing are taken from the external file e Salinity from SeaFET Data File Header The salinity value used for SeaFET data processing is taken from the SeaFET data file header e CTD Salinity from SeaFET Data Frames The salinity values used for SeaFET data processing are those from an attached SeaBird CTD instrument taken from the SeaFET data frames Note that 88 118 SeaFET Manual Recovery and Processing selecting this salinity source from a file that does not contain CTD salinity values will cause an error dialogue to open e Salinity The salinity value used for SeaFET data processing is entered manually The units are PSUs Output Data Files The processed data files are saved in a directory that can be selected using the Browse button The currently selected output directory is displayed in the text field next to the Browse button e Output Directory The directory where SeaFET processed data files will reside
52. for serial ports and USB virtual serial ports select the General tab and refer to the following SeaFET Connection Settings Default Baud Rate indicates the initial Baud rate that the SeaFETCom connect dialog will display when attempting to establish a connection To change the default Baud rate select a different rate from the drop down list Default Com Port indicates the initial serial communications port that the SeaFETCom connect dialog will display when attempting to establish a connection To change the default com port select a different serial port name from the drop down list Response Timeout indicates the number of seconds that SeaFETCom will wait for a response from SeaFET This timeout is used for establishing a serial connection and for most SeaFET commands Try increasing this timeout if SeaFETCom is unable to communicate with SeaFET File Listing Timeout indicates the amount of time that the SeaFETCom File Manager will wait for a response from SeaFET when requesting a listing of the files on the internal storage device Try increasing this value if File Manager is unable to list SeaFET data files Automatic Serial Connection indicates whether SeaFETCom will automatically connect with the default values both at program start and when the Connect button is pressed on the dashboard Preferences Ea General Display Message Logging SeaFET Connection Settings Default Baud Rate 9600 v Default Com Port COM1 X
53. hanges the zoom behaviour Zooming still occurs along the Time Axis for all plots but along the Range Axis for the clicked on plot only Click on the Time Series Graph outside the individual plots to recover the original zooming behaviour Zooming can also be accomplished by holding the left mouse button and selecting an area in the graph while dragging the mouse from left to right The graph is zoomed to the selected area on the release of the mouse button Moving the mouse from right to left while holding the left mouse button down zooms the graph back out The zoom functions are also available on a menu that pops up when the right mouse button is clicked over the graph Panning operations on the Time Series Graph are also supported They are available by pressing a modifier key while dragging the plot with the mouse On Windows the modifier key is the Control key while on the MacOSX it is the Alt key Time Series Graph Configuration The Time Series Graph can be configured by pressing the Select Sensors button or the Configure button 72 118 SeaFET Manual Integration with an External Pump The Configure Graph dialog allows the time axis range to be either unbounded or to be limited to a specified number of minutes When the time axis range size is limited the time series graphs will only display the most recent data values that are time stamped within the specified number of minutes The Select Sensors dialog provides the ability to
54. has elapsed If you enable the Repeat Auto Log after Interval option as well logging will automatically start logging again after the last data log has stopped and the specified interval time has elapsed Data Logging OR Frames Logged 0 Log Timer StartLog A Logging Options Log File Prefix SFET Log Directory C Data SeaFETCom Browse Previous Log File s Auto Logging Auto Log Duration 00 00 00 Repeat Auto Log after Interval 00 00 00 74 118 SeaFET Manual Configure Data File Headers Configure Data File Headers Select the Configure Data File Headers action to edit data file header records that are written by SeaFETCom to every logged sensor data file Three static headers are included by default e OPERATOR e EXPERIMENT e COMMENT Press the Add button to add a custom header Press the Remove button to remove the selected custom header Double click any Value cell to edit the value for the corresponding header Select the Prompt option to cause SeaFETCom to prompt for input of header record values whenever data logging is started Data Logging Headers Manual Value Headers Name Value Add OPERATOR user name EXPERIMENT Remove COMMENT V Prompt 75 118 SeaFET Manual Configure Data File Headers Acquisition Monitor The Acquisition Monitor can be found from the View menu item or it can be started by pressing the Error Details button o
55. hibits a Nernstian response to pH Martz et al 2010 Then V FETINT _ k oi k j i PH in se where R T In 10 S ners nernst F where R is the universal gas constant 8 314472 J K mol T is the temperature in K and F is the Faraday constant 96485 3415 C mol The constants kOi and k2i are the cell standard potential offset and temperature slope respectively and are provided as part of the instrument calibration pH From External FET EXT Cell The FET EXT cell also exhibits a Nernstian response to pH but presents the added complexity of being sensitive to the chloride activity V erer Koe koe T S PH a MH log Cly 2 108 uci logl l ta Hence the derivation of pH involves several steps to derive the chloride activity from the salinity These are outlined below Sample lonic Strength The sample ionic strength is calculated as Dickson et al 2007 y 19 924 5 1000 1 005 S where S is salinity psu Debye Huckel constant for activity of HCI 12 118 SeaFET Manual Overview This constant is calculated as Khoo et al 1977 A py 0 00000343 1 2 0 00067524 t 0 49172143 where t is temperature in C Total chloride in seawater Calculated as Dickson et al 2007 _ 0 99889 S C 35 453 1 80655 where S is salinity psu Logarithm of HCI activity coefficient Calculated as Khoo et al 1977 al Apy I _ 0 08885 0 000111 1 1 1 394 v J
56. ible multiple window interface for displaying key information relevant to the operating mode of the sensor and software The Dashboard Area always displays the Dashboard for connecting to SeaFET Other windows such as the Data Processing Dashboard can also reside in the dashboard area The Main View Area is where larger windows such as the Time Series Graph and the Processed pH Data Viewer appear when acquiring or processing data The Output Area mainly shows the Output window which shows diagnostic console outputs from the connected SeaFET and the software application itself A Status Area along the bottom of the main window shows information messages and progress reports as the software executes various actions Main View Area TE kiom 12453 e Menu TIT Cor onm Das Vow Wrens Heip Z2Oxd a SF saatr1Gom Danbor window B ee Sites Soe TESS a Gee Copec on Node TT Lane Lame one Fankas 2 ne tas W Reege cs X aka sions A Sore gue pree Preferences set SeaFETCom Preferences for display serial connection and data directory Time Series Loe Reta Lowered Aebi Dei Tone AES rds 107S WET God Tare May Wt Siu Aad Nive t saby Sas DIJA fetr Drone Sophy hen wae Mas Datar Se ta a 20 suk cd Bu tery aks oe aT oe hurtar a Fete 260 n Dashboard Area uman pk JX dsrk Beery A Tarai Siana Saks WabO lome lemts woes some Jm J0 WESI ai Tnte rks Ieee HIN pataxt lempe are Qa E Bom a Application Cow
57. ients extracted from the data file headers SeaFET data recorded by an external logger will not contain calibration header records and SeaFETCom will therefore be unable to reprocess it To work around this limitation you may supply coefficients via the SeaFET Calibration File input field on the SeaFETCom Data Processing Dashboard The format of the supplied calibration file is implied by the example below SeaFET Calibration Tue May 15 12 45 24 ADT 2012 HAFET _SERTAL_NUMBER 0006 EAFET_CAL OPERATOR Marlon Lewis RAFET CAL TIME STAMP 2012 04 27T17 27 27 0000 RAFET CAL PH_ TOTAL SCALE 8 10 RAFET CAL TEMPERATURE_C 21 25 HAFET CAL SALINITY_PSU 35 00 EAFET_CAL_PHINT_OFFSET_COEFF 9 231390E 02 EAFET_CAL_PHINT_SLOPE_COEFF 1 101228E 03 RAFET CAL PHEXT_OFFSET_COEFF 1 064598E00 EAFET_CAL_PHEXT_SLOPE_COEFF 1 048245E 03 wn NNNNNNNHnNN NN 85 118 SeaFET Manual Recovery and Processing Specify Temperature and Salinity Data The pH calculation is dependent on temperature and salinity SeaFET uses an internal thermistor and a user defined salinity constant for on board calculation The accuracy of the pH calculation can be improved by reprocessing in SeaFETCom software using temperature and or salinity inputs from external sources Temperature Salinity External File SeaFETC
58. if possible Otherwise the 99 118 SeaFET Manual Maintenance desiccants removed in Step 4 can be reused Reposition the battery plate and tighten the two nuts evenly until the plate is flush with the white connector Step 7 Reinstall the battery end cap Reconnect the battery connector making sure it locks in the receptacle With the vent plug still out replace the end cap while carefully guiding in the cable harness and lanyard making sure they are not pinched against the end cap Secure the end cap with the three 10 32 x 3 8 screws using a 5 32 hex driver Insert the vent plug fully Step 8 Verification Using a test cable USB or RS 232 with the external power leads connected to a live supply establish a connection to SeaFETCom Activate the internal batteries from the SeaFETCom dashboard and check that the voltage readings for the main and isolated battery packs are consistent with their nominal values 12V and 6V respectively if alkaline batteries are being used If either voltage is 100 118 SeaFET Manual Maintenance too low then it is possible that one or more batteries are not installed properly or are defective Re open the battery end cap and correct the problem Once finished deactivate the internal batteries for preserving power if desired and disconnect from SeaFETCom by selecting Advanced gt Disconnect for Storage from the Sensor menu bar SeaFETCom Dashboard Window Connection Mode Semp
59. ight Saving Time ADT is UTC 3 Satlantic is not open for business during the following holidays e New Year s Day January 1st Heritage Day The third Monday in February e Good Friday The Friday before Easter Sunday Easter Sunday is the first Sunday after the full moon on or following March 21 st or one week later if the full moon falls on Sunday Victoria Day The first Monday before May 25 th e Canada Day July 1st Civic Holiday The first Monday in August Labor Day The first Monday in September e Thanksgiving Day The second Monday in October e Remembrance Day November 11th Christmas Day December 25th 106 118 SeaFET Manual Data Formats Reference Data Formats Reference SeaFET outputs sensor data in ASCII text character format Data are packaged in frames Each frame consists of fields Fields are delimited separated by the comma character The first field of any frame is a synchronization header Every frame is terminated with a carriage return lt CR gt anda line feed lt LF gt 0x0D 0x0A Each field represents a number or a text using one of the following formats e ASCII Integer Al Example 245 e ASCII Float AF Example 0 832034 e ASCII String AS Example SATPHAO0001 SeaFET can be configured to output one of two available frame formats 1 Long ASCII Frame 2 Short ASCII Frame Long ASCII frame example SATPHA0001 2014083 13 0932646 7 80829 7 78879 20 5221 20 5038 3
60. ime from pump start to start of sampling Enable slave CTD control and false disable true enable on the fly TS corrections 115 118 SeaFET Manual Command Reference usectds Use CTD salinity for pH false true calculations usectdt Use CTD temperature for pH false true calculations ctdto CTD response timeout s 15 600 ctdpower Supply power to CTD when false true sampling NOTE Will use internal batteries or external power if available to power the CTD ctdtelem Replicate CTD data frames in false true SeaFET telemetry syncctd Enable periodic CTD clock false true synchronization Read only parameters e es Isolated battery pack voltage V rtcbattv RTC backup battery voltage V NOTE Every time this parameter is checked an extra amount of current is drawn from the RTC backup battery Keep reads to a minimum Electronics compartment relative humidity 116 118 SeaFET Manual References References T R Martz J G Connery and K S Johnson Testing the Honeywell Durafet for seawater pH applications Limnology and Oceanography Methods 8 172 184 2010 Dickson Sabine and Christian IOCCP Report No 8 2007 Khoo et al Determination of hydrogen ion concentrations in seawater from 5C to 40C standard potentials at salinities 20 to 45 Anal Chem 49 29 24 1977 R H Byrne G Robert Baldo S W Thompson and C T A Chen Seawater pH measurements an at sea com
61. inutes T 300s Each measurement consists of a burst of 9 frames bs 9 where each frame is an average of 10 measurements navg 10 To calculate the deployment duration first calculate the usable battery capacity for these conditions 65 118 SeaFET Manual Integration with an External Pump Qu 19800 mAh x 0 95 x 0 95 x 0 85 15189 mAh Where 0 95 accounts for the temperature de rating another 0 95 accounts for the self discharge over a year and 0 85 is the recommended safety factor Calculate the duty cycle D 3 5s 0 9 x 10 x 0 18 300s 0 0417 Finally substitute these into the deployment duration formulas Tdm 15 189 mAh 0 0417 x 30 mA 12151 h 506 days Tdi 15 189 mAh 1 0 0417 x 1 1 mA 14408 h 600 days The estimated deployment duration will then be 506 days Sample Calculation Il A SeaFET is to be deployed in 12 C waters on a 15 minutes schedule T 900s Each measurement consists of a burst of 9 frames bs 9 where each frame is an average of 10 measurements navg 10 The SeaFET will also control a CTD in order to perform on the fly temperature and salinity corrections The CTD will be powered from its own internal batteries so no additional power will be required from the SeaFET To estimate the usable capacity Qu 19 800 mAh x 0 92 x 0 95 x 0 85 14 710 mAh Where 0 92 accounts for the temperature de rating 0 85 accounts for the safety factor and a 1 year self disch
62. isplayed in SeaFETCom Enable Real Time Display is used to enable or disable the Real Time Display window that shows the latest acquired sensor data in numeric form This control does not affect the real time display of the Time Series Graph Disable the Real Time Display to improve performance on a slow computer Enable Data Acquisition Monitor indicates whether the Data Acquisition Monitor window is active Click the checkbox to enable or disable the Data Acquisition Monitor Disable the Data Acquisition Monitor to improve performance on a slow computer Enable Time Series Graph indicates whether the Time Series Graph is enabled or disabled Click the checkbox to enable or disable the Time Series Graph Disable the Time Series Graph to improve performance on a slow computer 40 118 SeaFET Manual Software x Bs Sensor Value Decimal Places 42 7 Use UTC Time V Enable Real Time Display 7 Enable Data Acquisition Monitor 7 Enable Time Series Graph 41 118 SeaFET Manual Software Message Logging The Message Logging panel allows for configuration of the way SeaFETCom writes errors warnings information and diagnostics messages to files Logging can be set to a range of verbosity levels The application message log files generated by SeaFETCom are crucial for diagnosing problems a Preferences mes a lt 3 General Display Message Logging Message Logging Logging Level IN
63. it enters Setup mode and SeaFETCom check the main and isolated battery voltages to determine if either is lower then their respective limit 8 0v and 4 0v acceptable for deployment The SeaFET may also have not been able to activate its internal batteries when connected via USB without being connected to an external power supply In either case the Internal Battery Voltage Too Low dialog is shown This dialog provides the user with the opportunity to connect an external power supply and then activate the internal battery by selecting the Retry button If the Ignore button is selected the user can proceed without activating the internal battery Internal Battery Voltage Too Low mtn i Low internal battery voltage detected Please ensure the internal batteries are connected and properly charged before deployment To connect the internal batteries now connect an external power supply and then press the Retry button Cree If SeaFETCom is exited when in Setup mode and SeaFET is in either Continuous or Periodic operational mode one of the following dialogs will request confirmation before leaving SeaFET in an autonomous operation mode 37 118 SeaFET Manual Software a SeaFET Autonomous Operation Mode Warning Se If main power is not connected the sensor will operate until the battery is exhausted Are you sure you want to exit SeaFETCom with this configuration Cegin j SeaFET Autono
64. les in Average 30 Number of Frames in Burst 1 Result A single averaged frame is transmitted The acquisition will take roughly 3 seconds 30 samples at 10Hz 3 You are confident that you understand the magnitude of the high frequency variance in pH and you want to discard this in order to simplify analyses See immediately above Integrating with a system controller Polled mode is ideally suited to the application involving the integration of SeaFET with a master system controller e g buoy controller CTD bearing serial port STOR X set opermode polled If the application is not telemetry bandwidth limited the system controller possesses a surplus of data storage and you wish to capture the high frequecny variance in the pH signal configure as follows Number of Samples in Average 1 Number of Frames in Burst 25 Transmitted Frame Format FULL_ASCII It is good practice to ensure that both science and engineering data are stored by SeaFET internally This is configured as follows Instrument Logging Frame Format FULL_ASCII When in Polled mode SeaFET will sleep until activity is detected on the telemetry port To wake SeaFET from sleep send any character on the telemetry port and then wait three 3 seconds for the wake sequence to complete You then have five 5 seconds to send an s character to command SeaFET to start a new sample Note that if the s is not sent within this five 5 second window SeaFET will retur
65. lies Specifications e On The Cover 9 118 SeaFET Manual Overview About SeaFET The SeaFET Ocean pH Sensor was developed by Dr Kenneth Johnson of the Monterey Bay Aquarium Research Institute MBARI and Dr Todd Martz of the Scripps Institution of Oceanography University of California San Diego Satlantic collaborated with MBARI and Scripps to make the instrument commercially available to researchers SeaFET uses innovative ISFET technology to measure pH in marine environments at depths up to 50 meters With its on board data storage capability and internal battery pack SeaFET can operate autonomously over long term deployments SeaFET has an optional capability of interfacing with a Sea Bird SBE37 CTD or an external pump When integrated with a SBE37 the SeaFET can perform real time temperature and salinity corrections and log oxygen concentration among other SBE37 parameters The supplied SeaFETCom software provides easy set up and configuration graphical real time data display for pre deployment checks and interactive sampling and data re processing to improve accuracy using ancillary temperature and salinity measurements 10 118 SeaFET Manual Overview Principle of Operation The primary sensor element of SeaFET is an ion sensitive field effect transistor ISFET This class of device has been used for pH sensing in industrial processes food processing clinical analysis and environmental monitoring Th
66. log Yuci j where ADH is the Debye Huckel constant for activity of HCI is the ionic strength and t is the temperature in C Acid dissociation constant of HSO4 Calculated as Dickson et al 2007 4276 1 Ks 1 0 001005 S e where S is salinity psu T is temperature K and is the ionic strength 1385 s3547 2 s 17 A 13856 394 57 47 986 In T V7 35474 268 p 76 r 28 2 i y 141 328 23 093 In T T T 771 54 114 723 In T 7 Total sulfate in seawater Calculated as Dickson et al 2007 0 1400 __S T 96 062 1 80655 where S is salinity psu 13 118 SeaFET Manual Overview Major Components SeaFET is encased in a cylindrical plastic housing that is robust and easy to handle A removable battery communications end cap is located on one end A sensor cap is located on the other end Both caps are secured with screws and sealed with O rings The battery end cap can be removed to replace the internal batteries Refer to section Battery Connection and Replacement for detailed instructions The battery end cap has a relief plug that is designed to release internal pressure in the unlikely event of an instrument flood or battery failure see section Safety and Hazards and to ease end cap removal The battery end cap also houses an indicator LED the magnetic switch sensor and a fallback push button on the inside that can be used in lieu of the magnet in c
67. mous Operation Mode Warni Ex p ing an If main power is not connected the sensor will operate using internal battery from Fri Dec 31 20 00 00 AST 1999 until Thu Dec 31 20 00 00 AST 2037 Are you sure you want to exit SeaFETCom with this configuration Acquisition Mode Once in Setup mode SeaFETCom can be used to start a data acquisition by pressing the Start button on the main dashboard This function causes the connected SeaFET to leave Setup mode and start sending data In Acquisition Mode incoming data can be viewed graphically and logged Disconnected State Disconnected state is not a mode like Setup Mode or Acquisition Mode Disconnected state indicates SeaFETCom has not established a connection to the sensor Only those functions that can be performed offline are available in SeaFETCom in Disconnected state Instead of loading information from the SeaFET these operations occur on the local file system resources Transition State Transition state indicates that SeaFET is currently not responsive because it is switching its internal operating mode If Transition state persists for more than a minute it likely indicates a communication problem Important Note Disconnecting USB When the USB cable is removed and main power ie internal battery is connected SeaFET will remain in the mode that it was last in 38 118 SeaFET Manual Software SeaFETCom Preferences To review and modify software preferences
68. n the Real Time Data view The Acquisition Monitor window shows the overall results of an acquisition It is useful in displaying problems that are occurring within the frame that SeaFET is outputting Data Acquisition Monitor Data Logging Frame Statistics Frame Id CheckSum Errors Counter Errors Status Errors Fittting Errors SATSFET LONG 0 o 0 0 SATSFET SHORT ol 0 0 0 Description of Fields The statistics are populated when an acquisition is active In most cases the number of erroneous frames are minimal or none This panel can be useful in determining when and why errors are occurring Frame Statistics e Frame ld The unique identifier of the frame in the Satlantic instrument package definition Read The number of valid frames read during an acquisition for a particular frame Errors The number of frames read that contained errors during an acquisition for a particular frame Checksum Errors The number of frames that contained checksum errors typically discarded Counter Errors The number of frames that contained counter errors typically not discarded Status Errors The number of frames that contained status errors typically discarded Fitting Errors The number of frames that contained fitting errors typically discarded 76 118 SeaFET Manual Recovery and Processing Recovery and Processing Topics in this chapter include e SeaFET Recovery e
69. n to the sleep state without sampling SeaFET will acknowledge receipt of a sampling command by echoing the s character followed by one or more frames of sampled data SeaFET will return to the sleep state when sampling is complete Long Duration Autonomous For long term autonomous deployment where power is the limiting resource configure SeaFET for Periodic operation mode Data files may be written to a single continuous file or may be written to daily log files whichever is most convenient for analysis Averaging should be implemented if you do not want to assess the high frequency component of the acquired signals Otherwise disable averaging and set the Number of Frames in Burst appropriately 59 118 SeaFET Manual Deployment Deployments of this nature may involve remote locations and costly ship time therefore considerable thought should be devoted to optimizing data quality yield with the available power Operational Mode Periodic Sample Interval 1hr Number of Samples in Average 1 Transmitted Frame Format FULL_ASCII Instrument Logging Frame Format FULL_ASCII Shipboard Power is generally not a limiting factor on shipboard applications Configure SeaFET to run in Continuous operating mode without averaging Set data transmission and logging to capture maximum sensor data and engineering data Operational Mode Continuous Number of Samples in Average 1 Transmitted Frame Format FULL_ASCII Instrument L
70. n to observe appropriate sampling protocols for pH An accurate external estimate of pH may be obtained through an implementation of the method developed by Byrne et al 1988 68 118 SeaFET Manual Integration with an External Pump Real Time Data Acquisition SeaFETCom can acquire data samples in real time from a connected SeaFET Acquired data and data statistics can be directed to the following destinations e The Time Series graph plots all acquired pH and temperature samples vs time e The Real Time Display shows the most recently acquired pH and temperature values in text format e The Acquisition Monitor counts number of data frames acquired and provides error statistics e Local log files captured data frames are written to a file Real time data acquisition via SeaFETCom is only possible when SeaFET is configured to operate in Continuous mode or Periodic mode Polled mode data acquisition is not supported in SeaFETCom See SeaFET Settings for more information on setting SeaFET operating modes Starting an Acquisition To start a data acquisition 1 Ensure SeaFET is powered by internal battery pack or external DC power supply 2 Connect SeaFETCom to SeaFET per instructions in Connecting to SeaFET section 3 In the General tab on the SeaFET Settings dialog ensure that Operational Mode is set to Continuous preferred or Periodic for pre deployment testing 4 Inthe Telemetry tab on the SeaFET Settings dialog ens
71. nected SeaFET is ready to deploy Serial Number identifies the connected SeaFET FW Rev reports the version number of the firmware running on the connected SeaFET The four buttons below the sensor information fields perform the following actions Connect Disconnect Connects and disconnects to a the SeaFET Sensor SeaFET Settings Change SeaFET settings Transfer Files Manage data and message log files on the SeaFET Start Stop Start and stop a data acquisition 36 118 SeaFET Manual Software Connection to SeaFET SeaFET has two main connection modes Setup and Acquisition Within each of these modes the functions available in SeaFETCom are different Below is a summary of connection and transition modes and available functions Setup Mode Setup mode is the administrative mode for the SeaFETCom application When the USB cable is plugged into the USB port on the host computer SeaFET will be powered via USB if main power ie internal battery is not connected The SeaFETCom Connect button is used to connect to SeaFET and enter Setup mode The length of time it takes for SeaFET to respond depends on the current state of SeaFET e If SeaFET was not connected to main power before connecting the USB cable it will take 3 5 seconds for SeaFET to initialize and connect e If SeaFET is already connected to main power and initialized the connection will be established within 2 3 seconds After connecting to a SeaFET
72. ng i e number of samples to average will also cause the log file name to increment System Messages Files The system message files contain system log information and are intended for diagnosing problems in the event of a sensor failure These files are stored in the LOG directory 83 118 SeaFET Manual Recovery and Processing Data Processing SeaFETCom can re process data files that have been off loaded from SeaFET to the local file system Re processing allows the input of ancillary temperature and or salinity measurements to calculate a potentially more accurate pH value than that produced by SeaFET which uses an internal thermistor and a fixed salinity value SeaFET Data Files Browse Processing Options V Enable Raw Data Checksum Validation SeaFET Calibration File Coefficients from SeaFET Calibration File Coefficients from SeaFET Data File Header A Specify Temperature Salinity Data Temperature Salinity External File Browse No Data Time Stamp Options E Offset 00 00 00 hhimmiss Temperature Options Temperature from External File Temperature from SeaFET Data Frames CTD Temperature from SeaFET Data Frames E Offset 0 00 Te Salinity Options Salinity From External File Salinity from SeaFET Data File Header CTD Salinity From SeaFET Data Frames Salinity 35 000 PSU 84 118 SeaFET Manual Recovery and Processing To Process Raw Files Select Da
73. nnect Deployment Cable After confirming battery condition and correct deployment settings using the test cable disconnect the test cable and connect the deployment cable If the instrument is being deployed autonomously install the dummy plug on the connector Secure the locking sleeve Deployment Tips It is recommended that the sensor be oriented horizontally If the instrument is mounted such that the electrodes face downward the accumulation of bubbles in the vicinity of the sensing elements may adversely affect measurement Similarly if the electrodes face upwards the accumulation of particulates may affect the instrument accuracy The ISFET used by SeaFET is known to exhibit a slight sensitivity to light This precludes any orientation that places the sensing elements in direct exposure to light This sensitivity may be diminished by the attenuation of light by the foul guard Mounting SeaFET in an orientation that places the sensing elements facing upwards is not recommended Stagnant low flow environments present challenges to many potentiometric measurement systems Care should be taken to validate sensor performance in low flow environments where possible prior to long deployments Validate It is standard practice to validate performance while SeaFET is deployed Where possible water sampling in the vicinity of the sensor should be performed at the beginning of a deployment and near the end of a deployment Care should be take
74. nti Isolsted Battery Yokage 0 1 Sample Averaging Number of Samples n Average 10 Serial Kumbar 339 P i Rev 3 6 0 Number of Frames in Bursts 30 n i Opbonal Sample Date Range J Connect Battery Enable Sampling winds Bayn sampling on this date 2000 01 91 ure y bey i a Seep sampling on tisdae 2086 01 01 lute 3 SeT Stins p Irtemal Device Logging af Transfer Files Loggng Level Iro D R Masimum Log Fle Sa 1024 KB Qs 0 59 3 2090 35 200020 200025 Depkyment haradkeristics Real Time Display SeaFET0333 E Estimated Frame Rate 1 00 framesjsaz Estimated Battery Lie 11 days Select Sensors el Output Data Lognina Femmated Total Samples 91300 fl puna pie ints pppication console Estimated Effective Interval mirates DHONT ai aF pH EXT oH Estimated Sample Curation mrates Temperature fe We Acquisition Information 40 paagi Upload Canna Dafast Help om orto Lene re 70m TRUE SeaPRIeget ctdto get etdro on 120 Gearet 25 118 SeaFET Manual Software Installing SeaFETCom For the latest SeaFETCom software updates please visit http satlantic com seafetcom Installing SeaFETCom on Windows Supported Microsoft Windows systems XP Vista 7 8 32 bit or 64 bit Minimum recommended computer hardware e Processor 2 6 GHz Intel Pentium IV or equivalent e Memory 2 GB e Disk space 1 GB of free disk space To install the software run the SeaFETCom self extra
75. of these factors provided by some example calculations will help in deployment planning The SeaFET operates from a single battery stack which is internally divided into two independent battery packs e Main battery pack used for supplying power during sampling e Isolated battery pack used for supplying power to the sensing element while in standby When calculating battery endurance both packs need to be accounted for Calculating Usable Battery Capacity The SeaFET internal battery compartment holds 12 Alkaline D Cell batteries The nominal capacity specified by the battery manufacturer is attained under ideal operating conditions To calculate deployment duration the user should consider the usable capacity which is calculated from the nominal capacity and takes into account e Operating Temperature Usable capacity decreases at lower temperatures A 1 per C below 20 C de rating is recommended e Battery Self Discharge A battery capacity is continuously reduced due to self discharge effects A 5 per year de rating is recommended e A Safety Factor A safety factor of 15 is recommended when calculating usable capacity NOTE The temperature and self discharge de rating guidelines are specified for alkaline batteries Consult the battery manufacturer documentation if using a different chemistry Sample Calculation For a six month deployment in 12 C waters using a 19800 mAh alkaline battery pack nominal capacity f
76. ogging Frame Format FULL_ASCIl 60 118 SeaFET Manual Integration with a SBE 37 CTD Optional Feature Integration with a SBE 37 CTD Optional Feature The SeaFET has the optional ability to be integrated with a SBE 37 CTD SeapHOx mode in order to perform accurate real time temperature and salinity corrections and to log oxygen concentration among several other SBE 37 parameters Refer to the Data Formats Reference for information on available parameters CTD Configuration Prior integration with the SeaFET the CTD needs to be configured so that it operates at the right baudrate outputs data in a format the SeaFET can understand and reports temperature and salinity in the right units The CTD pumping time also needs to be adjusted for proper interoperation The following CTD settings must be ensured for proper interoperation Refer to the CTD manual for instructions on how to change these parameters Baudrate BaudRate 9600 e Output format OutputFormat 2 Enable temperature OutputTemp Y e Enable salinity OutputSal Y Enable oxygen OutputOx Y e Enable pressure OutputPress Y e Output units SetCoastal 0 e Pumping AdaptivePumpControl N OxNTau 7 WARNING The CTD needs to be configured for interoperation with the SeaFET prior integration Failure to configure the CTD adequately may result in invalid measurements A pre deployment test is highly recommended to make sure the CTD data is being ingested by the Sea
77. ok Setup Cosel Acquisition Commute s Status Area Output Area Menu The following is a summary of all actions available on the SeaFETCom main menu SeaFETCom menu lists actions for setting software preferences Exit halt and exit SeaFETCom Sensor menu lists actions for connecting to SeaFET and configuring it for operation 31 118 SeaFET Manual Software Connect Disconnect initiates or terminates the connection to SeaFET Same as the Connect Disconnect button on the dashboard See Connecting to SeaFET for more information Start Stop starts or stops Real Time Data Acquisition activities on SeaFET and real time display and logging of data by SeaFETCom Same as the Start Stop button on the dashboard This item is only enabled when there is an active connection to SeaFET SeaFET Settings shows the SeaFET Settings dialog for configuring the SeaFET This item is only enabled when there is an active connection to SeaFET Transfer Files shows the Transfer Files dialog for transferring files from the SeaFET to your computer This item is only enabled when there is an active connection to SeaFET Set Clock shows the Set Clock dialog to synchronize the SeaFET internal clock with the host computer clock This item is only enabled when there is an active connection to SeaFET Summary Report generates a PDF Summary Report of SeaFET settings and status This item is only enabled when there is an active conne
78. ole shows the Application Console in the Output Window Real Time Data shows the Real Time Display window Acquisition Monitor shows data acquisition statistics in the Data Acquisition Monitor window Window menu provides actions for resizing and relocating internal windows Close Window removes the selected window from view Close All Documents closes all non dashboard windows Configure Window provides options for changing the selected window Reset Windows returns all windows to their default location Customizing SeaFETCom Layout SeaFETCom provides a flexible multiple window interface for customizing the layout of most components Windows can be viewed dragged tabbed docked and stretched to best suit the job at hand within the available screen size To move a window to an alternate location 1 Click and hold the top bar on the window 2 Drag it within its own area or to a different area 3 Move the window around near the desired location until an orange rectangle frame appears 4 If the orange rectangle fully covers an existing window the dragged window will be tabbed within it 5 If the orange rectangle partly covers and existing window the existing window will be resized to make room for the dragged window to locate adjacent 6 Release the mouse button to place the window in its new location To resize a window 1 Roll the mouse pointer over an edge of the internal window until the pointer changes to a double ended arr
79. ole shows the sensor data as it is transmitted by SeaFET while in Acquisition Mode The Acquisition Console does not log acquired sensor data directly See 34 118 SeaFET Manual Software Dashboard The SeaFETCom dashboard displays SeaFET connection status and provides actions for managing SeaFET The top section of the dashboard shows whether a SeaFET is connected and if connected some key SeaFET status information The info fields are populated when the SeaFET is attached and communication has been established SeaFETCom Dashboard Window Connection Mode Semp Connection Status Connected Available Disk Space 3 550 MBytes 94 SeaFET Clock Time 05 Sep 2014 18 03 28 UTC Power Supply Voltage 11 837 Main Battery Voltage 11 7 Isolated Battery Voltage 11 7 Deployable Status Ready to Deploy Serial Number 999 FW Rev 3 6 0 Erea SeaFET Settings a Transfer Files Start Connection Mode displays the current mode of SeaFETCom operation relative to connection with SeaFET e Disconnected No active connection to SeaFET Indicated by a red background e Transition SeaFETCom is attempting to command SeaFET to transition to Setup mode Indicated by a yellow background e Setup SeaFET is idle awaiting commands from SeaFETCom Indicated by a green background e Acquisition SeaFET is acquiring data in either Continuous or Periodic acquisition mo
80. om accepts time correlated temperature and salinity data in one of two supported file formats 1 Generic CSV Comma Separated Values text file 2 Sea Bird Electronics cnv converted CTD data format Select the temperature salinity external file using the Browse button The selected file is displayed in the text field and a data loaded icon will appear when data loading is complete Temperature Salinity CSV File SeaFETCom accepts data from a CSV file in the following format YYYY MM DD hh mm ss lt temperature gt lt salinity gt lt cr gt lt lf gt Where e YYYY MM DD hh mm ss is the UTC date and time that the temperature and salinity sample was collected lt temperature gt is the measured temperature in degrees Celsius in floating point format lt salinity gt is the measure salinity in PSU in floating point format e lt cr gt lt lf gt are the carriage return and linefeed characters to indicate end of line Fields must be separated by the comma character This is an example of a valid file 2012 04 25 15 22 48 10 8326 34 8974 2012 04 25 15 22 54 10 8547 34 895 2012 04 25 15 23 00 10 8517 34 9032 2012 04 25 15 23 06 10 867 34 9007 2012 04 25 15 23 12 10 8889 34 8926 86 118 SeaFET Manual Recovery and Processing There are many utilities and editors available that can be used to convert temperature and salinity data to the above required format For scripted conversion of large data sets tools such as GN
81. or Panasonic LR20XWA the usable capacity will be Qu 19800 mAh x 0 92 x 0 975 x 0 85 15100 mAh Where 0 92 accounts for the temperature de rating 8 C below 20 C 0 975 accounts for a 2 5 six month self discharge and 0 85 accounts for the recommended 15 safety factor Endurance Calculations Periodic Mode 64 118 SeaFET Manual Integration with an External Pump Use the following formulas to estimate the deployment duration Td for a given deployment configuration in periodic mode The formulas provide an estimated duration for each internal pack main and isolated The overall deployment duration will be the lowest of the two For the main battery pack Tdm Qu D x la For the isolated battery pack Tdi Qu 1 D x Is Where e Td Deployment duration in h e Qu Usable capacity in mAh e Is Sleep current 1 1 mA e la Active current 30 mA e Duty cycle calculated as D tboot tpump bs x navg x tsample T Where e tboot Boot from sleep time 3 5 s e toump CTD pumping time recommended 35s e bs Burst size e navg Averaging size e tsample 1 sample time 0 1 s e T Periodic sampling interval in s Note that T bs and nAvg are user selectable parameters On the other hand Is la tboot and tsample are inherent characteristics of the SeaFET Sample Calculation I A SeaFET without a slave CTD is to be deployed in 15 C waters taking measurements every 5 m
82. ow 2 Click drag and release to set the new window size To undock a window 33 118 SeaFET Manual Software 1 Click and hold the top bar on the window 2 Drag it outside the area of the main window 3 Release to undock the window into its own main window 4 Alternately select Window gt Dock Window on the menu 5 Select Window gt Dock Window on the menu to return the window to its internally docked location Output Window SeaFETCom provides logging facilities that can be used to troubleshoot problems that may arise on the host computer or on SeaFET While the application is running there are three logging consoles that reside in the Output window Output x wye Application Console x Setup Console x Acquisition Console x Ok 2012 03 29 18 27 17 A SeaFET gt get disktotal get disktotal Ok 1962770432 SeaFET gt get diskfree get diskfree Ok 1962442752 SeaFET gt get mainvolt get mainvolt Ok 13 637 SeaFET gt mW Application Console displays a log of all the actions performed by the SeaFETCom application It also records any errors or warnings that may occur while communicating with SeaFET It also displays all output from SeaFET when in Setup mode see below All Application Console messages are logged to a local file as described in the Message Logging section Setup Console displays all output generated by SeaFET as it executes commands in Setup mode Acquisition Cons
83. p O ring grease should not be used in the vicinity of the ISFET sensing element and external reference electrode Place the wet cap with O ring over the ISFET and external reference electrode ensuring that the O ring is in contact with the end cap face Ensure that the O ring fits snugly in the wet cap groove and will not be pinched If the cap is to be used as a flow cell make sure it is installed as shown in the figure below This orientation will ensure an appropriate liquid flow through the sensing elements Secure the wet cap to the end cap with three 10 32 x 5 8 screws using a 5 32 Hex driver or Allen key The wet cap should now be securely fastened to the instrument end cap and is ready to be filled with artificial seawater Through any of the wet cap holes pour sterilized artificial seawater with suitable spouted glassware a funnel or a syringe Fill void space completely Insert and secure the plugs one at a time Ensure that a reliable seal has been established You may need to expel a very small quantity of water to facilitate the insertion of the last plug Wipe the instrument housing and wet cap surfaces dry of any excess artificial seawater 93 118 SeaFET Manual Maintenance Flow Cell Orientation 94 118 SeaFET Manual Maintenance Preventative Maintenance WHEN THE INSTRUMENT IS NOT IN SERVICE THE WET CAP MUST BE IN PLACE AND FILLED WITH AN APPROPRIATE STORAGE SOLUTION
84. pH calculation and reprocessing Satlantic recommends that your SeaFET be returned to our facility for recalibration on an annual basis Satlantic additionally recommends that you periodically monitor the the accuracy of your SeaFET calibration via comparison of calculated pH values with independently measured pH samples taken shortly before and after deployments either in situ or through direct measurements of a primary standard under temperature controlled conditions Note that the SeaFET is shipped with a calibration performed at 0 5m depth Since the ISFET sensor exhibits a pressure sensitivity this calibration is only valid for near surface deployments For obtaining accurate measurements at deeper deployments Satlantic recommends that independent pH samples are taken in situ shortly before and after deployment in order to apply an offset correction 102 118 SeaFET Manual Maintenance Firmware Upgrade Satlantic may occasionally release new SeaFET firmware to provide fixes or improvements To upgrade SeaFET firmware using a firmware file provided by Satlantic 1 Select Sensor gt Advanced gt Upload Firmware File from the SeaFETCom main menu 2 Press the Browse button to locate the supplied SeaFET firmware file 3 Press the Upload button to start the firmware upload 4 Wait until SeaFET is returned to Setup Mode This can take about one minute Upload Firmware File Ea SeaF T Firmware File Cautions
85. parison of spectrophotometric and potentiometric methods Deep Sea Research 35 8 1405 1410 1988 T D Clayton and R H Byrne Spectrophotometric seawater pH measurements total hydrogen ion concentration scale calibration of m cresol purple and at sea results Deep Sea Research 40 10 2115 2129 1993 K J Kroeker F Micheli M C Gambi and T R Martz Divergent ecosystem responses within a benthic marine community to ocean acidification Proceedings of the National Academy of Sciences of the United States 108 35 14515 14520 P G Matson T R Martz and G E Hofmann High frequency observations of pH under Antarctic sea ice in the southern Ross sea Antarctic Science 23 607 614 2011 P C Yu and G E Hoffman P G Matson T R Martz The ocean acidification seascape and its relationship to the performance of calcifying marine invertebrates Laboratory experiments on the development of urchin larvae framed by environmentally relevant pCO2 pH Journal of Experimental Marine Biology and Ecology 400 288 295 2011 117 118 Index A About SeaFET 10 Acquisition Display 71 Acquisition Monitor 76 B Battery Endurance 64 Battery Replacement 96 C Calibration 102 Cautions and Hazards 4 Command Reference 113 Connecting to SeaFET 37 Contact Satlantic 106 CTD Settings 54 D Data Formats Reference 107 Data Logging Headers 75 Data Processing 84 Data Recovery 80 Deployment 57
86. r consumption 62 118 SeaFET Manual Integration with an External Pump Integration with an External Pump For applications in which water circulation is required the SeaFET has the ability to control an external pump To this end the SeaFET features a switched 12V output that can be connected to the power input of an external pump see PUMP V in External Interfaces section Note that V would also have to be connected to the pump negative input Typically the SeaFET would be configured to pump before or during sampling Different deployment configurations will require different pumping times Refer to the External Pump Settings section for information on how to configure the pumped operation Note that pumping will impact the power consumption performance by increasing the active current and the time the SeaFET is active during sampling Satlantic recommends using the Sea Bird 5P submersible pump Other pumps could be considered provided they can be powered from 12V do not drain more than 650mA continuously and provide sufficient flow 63 118 SeaFET Manual Integration with an External Pump SeaFET Battery Endurance Introduction This section provides guidance for estimating battery powered deployment duration SeaFET battery life is a function of battery conditions such as age and temperature power consumption characteristics of the instrument and the sampling schedule selected by the operator An understanding
87. rame 3 NONE Turns off SeaFET data logging SeaFET will not record measurement data on internal storage Log File Creation Method determines when SeaFET creates a new file for logging data internally e Daily a new file is created each day at 00 00 00 UTC e By Sample Event a new file is created for each new data acquisition sampling event This is useful for creating a separate file for each profile when in profiling mode e By File Size a new file is created when the current file reaches the specified Maximum Size Maximum Size in KB kilo bytes that the active SeaFET internal data log file is allowed to reach before a new one is created This only applies when the Log File Creation Method is set to By File Size 51 118 SeaFET Manual Settings Processing Settings For every measurement frame logged and transmitted SeaFET calculates pH values for internal and external sensors To calculate pH SeaFET applies factory calibration coefficients temperature from the on board thermistor and a user configurable salinity value that roughly approximates the salinity of the water being sampled To adjust the salinity value used for on board pH calculation select the Processing tab of the SeaFET Settings dialog Type the desired ambient salinity value and press Upload to pass it to SeaFET Sea ET Settings Ea General Telemetry Processing External Pump CTD On board Salinity Salinity BS 000 psu
88. rated possesses a Surplus of data storage configuration should involve the following Telemetry Settings Transmitted Frame Format FULL_ASCII Instrument Logging Frame Format FULL_ASCII This enables the transmission of the full data frame which includes both science data e g time pH temperature CTD and engineering data e g battery voltage internal humidity etc The engineering data are useful in assessing the state of health of the instrument Averaging and Burst Sampling SeaFET can be configured to reduce measurement noise by averaging a number of samples before outputting a frame of data Additionally in Periodic or Polled mode the number of frames averaged or not per burst event can be set These SeaFET Settings affect the volume of data output by the sensor and the power consumed during measurement You may wish to configure how SeaFET performs averaging and burst sampling for the following reasons 1 To capture the high frequency variance in the pH signal set Number of Samples in Average 1 Number of Frames in Burst 30 Result Thirty non averaged frames are transmitted per measurement Frames within the burst are transmitted at a frequency of approximately 10Hz 58 118 SeaFET Manual Deployment 2 You want to adequately sample pH and temperature however the transmission of large volumes of data is prohibited by monetary cost limited bandwidth or limited external data storage set Number of Samp
89. readings Even while the instrument is not sampling its sensing element requires a continuous current flow for measurement stability purposes This power is drawn from the internal batteries To preserve battery power after the instrument is retrieved consider deactivating the battery pack using the magnetic switch or through SeaFETCom Note however that a sensing element may take up to 24 hours to IMPORTANT warm up and provide reliable readings after it has been re powered and deployed To place SeaFET in low power stand by mode so that warm up is not required 1 Connect via SeaFETCom Dashboard 78 118 SeaFET Manual Recovery and Processing 2 Select Polled mode in SeaFET Settings 3 Disconnect via SeaFETCom Dashboard Visual Inspection Visually assess the sensing elements Look for particulates Look for erosion of the reference electrode Inspect the sensing head of the instrument Look for particulate deposits in the vicinity of the ISFET and reference electrodes Assess whether the surface of the reference electrode has undergone any corrosion or whether any deposits appear Inspect the annular ceramic frit located at the base of the protrusion on which the ISFET is located Ensure that the frit is not fouled it should be white or slighty off white in color Note all such qualitative observations to aid in future quality assessment of the data In the event that either the ISFET or the reference electrode req
90. rip pull it out with one hand A safety lanyard anchors the end cap to the battery plate This lanyard prevents accidentally pulling off the battery end cap connector wires when removing the end cap 97 118 SeaFET Manual Maintenance Step 4 Remove the battery plate Disconnect the white battery endcap connector by pressing its locking tab and gently pulling off Remove the desiccant packs and preserve them in a sealed bag Loosen and remove the two 1 4 nuts that secure the battery plate When loaded the battery plate compresses six springs that hold the battery stacks To prevent the plate from locking when removing it loosen both nuts at the same time ex alternate loosening a few turns and switching to the other nut Loosen and remove 2 x 1 4 nuts 98 118 SeaFET Manual Maintenance Step 5 Replace the batteries Remove and dispose appropriately the old batteries Change all batteries at the same time and never mix new and old batteries or different battery chemistries We recommend using industrial 1 5V alkaline D Cells Load the compartment with new batteries according to the polarity indicated in the compartment labels Step 6 Reinstall the battery plate Inspect clean and lubricate if necessary the O rings on the batery end cap Inspect and clean the surface on the inside of the battery compartment where the O rings sit At this point it is advisable to replace the desiccant packs for fresh ones
91. s the Estimated Sample Duration Estimated Deployment Samples Displays the estimated number of samples that will be logged during deployment of the instrument The deployment samples is dependent on the estimated frame rate the number of sampling events and the duration of each sampling event Estimated Effective Interval Displays the estimated effective sample interval in minutes for Periodic Operational Mode The effective sample interval is based on the Sample Interval setting except when the estimated sample duration exceeds the selected Sample Interval Estimated Sample Duration Displays the estimated sample duration in minutes for Periodic Operational Mode The sample duration is based on the Number of Samples in Average and the Number of Frames in Burst settings 49 118 SeaFET Manual Settings Telemetry Settings SeaFET Settings s General Telemetry Processing External Pump CTD Data Transmission Serial Baud Rate 57600 X Transmitted Frame Format FULL_ASCII v Tra sages Data Logging Instrument Logging Frame Format SHORT_ASCII v Log File Creation Method By Sample Event v Maximum Size 1024 KB Upload Cancel l Default Help Data Transmission Settings Serial Baud Rate setting configures the transmission rate of the SeaFET RS 232 interface Possible baud rates include e 9600 e 19200 e 38400 e 57600 e 115200 Transmitted Frame Format sets the data format transmitted by S
92. ssing The status of the processed values 0 No Error Status Check Sum The verity byte frame check sum SeaFET Processed ASCII Data Frame Format 91 118 SeaFET Manual Maintenance Maintenance Topics in this chapter include e Storage and Shipping e Preventative Maintenance e Battery Replacement e Calibration e Firmware Upgrade 92 118 SeaFET Manual Maintenance Storage and Shipping WHEN THE INSTRUMENT IS NOT IN SERVICE THE WET CAP MUST BE IN PLACE AND FILLED WITH AN APPROPRIATE STORAGE SOLUTION DO NOT ALLOW THE WET CAP STORAGE SOLUTION TO FREEZE DURING SHIPPING OR STORAGE THIS WILL DAMAGE THE DURAFET AND VOID THE WARRANTY SeaFET is shipped with the wet cap installed The wet cap is filled with UV sterilized artificial seawater salinity equivalent to 35 ppt after Kester et al 1967 immersing the sensing element and reference electrodes If the sensor is taken out of service and is to be stored follow the procedure below Note that the wet cap must be installed and filled even for brief periods out of service i e minutes Wet Cap Flow Cell Installation 1 Place the instrument on a flat surface with the sensor end cap on a side Secure the instrument to prevent it from rolling and possibly falling Sitting the tube end on pliers handles can quickly provide a secure lock If the foul guards are in place remove them Fit the wet cap O ring in the groove on the bottom of the ca
93. t SeaFET by pulling it from the cable This can cause damage to the bulkhead connectors cables and splices Dummy connectors should always be replaced as soon as SeaFET is retrieved This will help protect the bulkhead connector from dirt and damage Always rinse SeaFET with sterile artificial sea water prior to storage Damage resulting from failure to do so is not covered under warranty Refer to the Maintenance section of this manual for instructions Do not leave SeaFET in direct sunlight on deck when it is not being used Direct sunlight can can damage SeaFET by overheating it When deploying SeaFET in water do not leave it or any other instrument unattended Boat drift can entangle the cable and cause damage or instrument loss 4 118 SeaFET Manual Cautions And Hazards Pressure Hazard Electrical Hazard DANGER If you suspect that the instrument has flooded use EXTREME CAUTION around the instrument If the instrument leaked at depth it might remain pressurized when recovered and cause the end cap to be launched from the pressure case with extreme force If you suspect a flood make sure to check the instrument for signs of pressurization If the instrument is pressurized you may notice the gap between the end cap and pressure case look to be extended To relieve the instrument pressure stand to the side of the instrument Relieve the pressure by VERY slowly removing the pressure relief plug using a p
94. t at different rates and that leads to a separation of charge Unfortunately this potential is not measurable or knowable and will contribute to the uncertainty of the pH reading The external cell also consists of the ISFET as the working electrode The potential of the external reference electrode is expected to vary with the chloride concentration of the sensed medium In this sense it is sometimes termed a pseudo reference electrode Ordinarily this would not be a good approach for measuring pH because the signal exhibited by the overall cell potential will be the sum of a chloride signal and a hydrogen hydroxide ion signal ISFET sensitive to H OH Notwithstanding in seawater the chloride concentration can be approximated from salinity and the chloride signal estimated in order to retrieve hydrogen hydroxide ion signal The external reference electrode has been incorporated into the design because among other considerations it does not have a liquid junction potential This results in a more accurate and stable reading provided that the chloride concentration of the sample can be accurately determined 11 118 SeaFET Manual Overview pH Calculation This section provides a brief description of how the SeaFET derives pH from the internal and external cells voltage readings sample temperature and sample salinity More details can be found in the references here cited pH From Internal FET INT Cell The FET INT cell ex
95. ta gt SeaFET Data Processing from the main menu to show the data processing panel Select SeaFET Data Files Press the Browse button to locate and select one or more raw files to place in the SeaFET Data Files list Any files already in the list are replaced by this action All files placed in the list are initially selected highlighted for later processing You can select or deselect individual and multiple files in both the Select Data Files dialog shown by the Browse button and in the SeaFET Data Files list on the processing panel There are several ways to change which files are selected e Click on a file to select it and de select all others e Hold lt Ctrl gt and click on a file to toggle its selection state without affecting other selected files e Hold lt Shift gt and click on a file to select a range of files e Hold lt Ctrl gt and lt Shift gt to select a range of files without affecting other selected files e Up down arrow keys can be used instead of mouse click Specify Calibration Coefficients Each SeaFET is individually factory calibrated to compensate for sensor variations Calibration coefficents are stored on the device and are applied by SeaFET to on board pH calculations Every data file logged by SeaFET or SeaFETCom provides header records that specify the calibration coefficients in effect at the time of acquisition When re processing a logged data file SeaFETCom by default applies the calibration coeffic
96. te the internal batteries approach the magnet to the target until the indicator LED starts flashing green Remove the magnet as soon as you notice the green flashes Deactivating the internal batteries To deactivate the internal batteries approach the magnet to the target leave it for a second and remove it The indicator LED will flash red acknowledging the deactivation request and the batteries will next be deactivated If the red flashes are not displayed repeat the operation No power will be drawn from deactivated batteries Magnetic Switch Target Indicator LED 19 118 SeaFET Manual Overview Power Supplies The SeaFET operates from two distinct sources of power e Internal batteries e External power input VIN Understanding the purpose and function of each power source is fundamental for the successful operation of the instrument An incorrect power setup could lead to invalid deployment data Internal batteries The SeaFET battery compartment holds 12 Alkaline D Cell batteries These are internally split into two packs e Main battery pack 12V nominal e Isolated battery pack 6V nominal The Main battery pack is used to power the instrument control electronics when the instrument is in active mode while the Isolated battery pack is used to power the sensing element when the instrument is in low power standby mode A distinctive characteristic of the SeaFET is that it requires an uninterrupt
97. tenance 92 Storage and Shipping 93 Preventative Maintenance 95 Battery Replacement 96 Calibration 102 Firmware Upgrade 103 Troubleshooting 104 Contact Satlantic 106 Data Formats Reference 107 Using a Terminal Emulator 111 Command Reference 113 References 117 Index 118 SeaFET Manual Cautions And Hazards Cautions And Hazards SeaFET has sensitive components that can be damaged by improper storage and handling SeaFET may become highly pressurized during deep deployment and could cause personal injury if not properly depressurized SeaFET contains a battery pack that may present an electrical hazard if improperly handled Ensure that all instrument users have read and understood all cautions and hazards cited in this section Cautions SEAWATER ONLY WHEN SEAFET IS NOT IN SERVICE THE WET CAP MUST BE IN PLACE AND FILLED WITH CLEAN SEAWATER IMMERSING THE SENSING ELEMENTS IN FRESH WATER CAN LEAD TO SENSOR INSTABILITY AND DAMAGE Do not allow the DuraFET KCI gel or the wet cap filling solution to freeze during shipping or deployment This will damage the DuraFET and void the warranty Never let the sensing elements dry out If SeaFET is to not to be redeployed immediately put the wet cap in place and fill it with artificial sea water The ISFET is light sensitive and will produce a voltage offset if illuminated If the SeaFET is deployed with the flow cell the flow cell should be shaded e g using tape Never lif
98. to do so will result in unusable data Batteries can be activated from the SeaFETCom dashboard or by using the magnetic switch In order to ready an instrument for operation from storage or from the state in which the instrument was shipped the wet cap must be removed the foul guard must be installed and the deployment cable connected These procedures are outlined below Remove Wet Cap 1 Remove the two stainless steel plugs from the Wet Cap Set aside for future wet cap use 2 Invert the instrument to pour the storage solution artificial seawater from the wet cap into a sink or vessel This procedure will be easier if the cable is not connected Return the instrument to its initial orientation 3 Using a 5 32 hex driver or Allen key remove the three 10 32 x 5 8 socket head cap screws from wet cap Set the screws aside for anti fouling guard installation 4 Remove the wet cap ensuring that the associated O ring is retained for future use 5 Wipe the instrument housing and wet cap surfaces dry of any excess artificial seawater Install Foul Guard 67 118 SeaFET Manual Integration with an External Pump 1 Place the instrument on a flat surface with the connector sensor end cap up 2 Place the electrode foul guard over the ISFET probe and external reference electrode 3 Insert three 10 32 x 5 8 socket head cap screws removed from the wet cap and tighten completely using a 5 32 hex driver or Allen key Co
99. uires cleaning please refer to Preventative Maintenance 79 118 SeaFET Manual Recovery and Processing Data Recovery The SeaFET stores sensor data and log files on its internal drive Note that the date and times associated with the files are UTC times USB Mass Storage The most efficient method of retrieving large numbers of files from SeaFET is via the USB Mass Storage interface 1 Connect USB programming cable to the SeaFET USB bulkhead connector 2 Connect USB programming cable to any available USB port on your computer 3 Find the mounted SeaFET drive on the computer s Desktop or via the computer s file explorer program 4 Select desired files from the SeaFET drive 5 Copy paste or drag drop the selected files to a local folder The SeaFET USB Mass Storage interface is read only You cannot delete files from SeaFET internal storage via USB Mass Storage Use the SeaFETCom File Manager to delete unwanted files from SeaFET internal storage File Manager To use the SeaFET File Manager you must first connect to SeaFET via RS 232 COM port or USB virtual COM port After connection is established press the Transfer Files button on the SeaFETCom Dashboard to show the File Manager dialog 80 118 SeaFET Manual Recovery and Processing File Manager Data Files Local Filesystem Instrument Filesystem C Data SeaFETCom Browse Name Date Size Type P 1 E 14085
100. updated software by looking on your computer on the hardware installation CD or on the Windows Update Web site with your permission Read our privacy policy Can Windows connect to Windows Update to search for software Yes this time only C Yes now and every time connect a device Click Next to continue lt Back Cancel Press the Next button to proceeed Found New Hardware Wizard This wizard helps you install software for SeaFET CDC Virtual COM Port If your hardware came with an installation CD lt 4 or floppy disk insert it now What do you want the wizard to do Click Next to continue lt Back Cancel After the second dialog another dialog is displayed to warn that the USB Serial Driver publisher can t be verified Select the Continue Anyway button to safely install the Satlantic USB Serial Driver 28 118 SeaFET Manual Software Hardware Installation N The software you are installing for this hardware SeaFET CDC Virtual COM Port has not passed Windows Logo testing to verify its compatibility with Windows XP Tell me why this testing is important Continuing your installation of this software may impair or destabilize the correct operation of your system either immediately or in the future Microsoft strongly recommends that you stop this installation now and contact the hardware vendor for software that has passed Windows Logo testing STOP
101. ure that Transmitted Frame Format is set to FULL_ASCII 5 Press the Start button on the dashboard 6 If SeaFET is in Periodic operating mode press OK on the Periodic Acquisition dialog that shows the next periodic sampling start time When a SeaFET is connected to SeaFETCom an acquisition can be started by pressing the Start button if no internal battery is present SeaFETCom will prompt to apply external power When starting an acquisition within SeaFETCom the graphical data display allows monitoring of the generated data in real time Before deployment it is advisable to confirm that the generated data are within the expected range The procedure to acquire real time data via SeaFETCom is slightly different for the following Operational Modes 69 118 SeaFET Manual Integration with an External Pump Continuous When the Acquisition Start button is pressed SeaFETCom commands SeaFET to exit Setup mode and begin emitting frames of data The data frames are acquired by SeaFETCom until the Acquisition Stop button is pressed Periodic When the Acquisition Start button is pressed the Periodic Acquisition dialog is opened to display the SeaFET clock time and the start time of the next periodic acquisition event Then SeaFETCom commands SeaFET to exit Setup mode and does not start acquiring data frames until it is time for the next periodic acquisition event The duration of each periodic acquisition event is based on the burst s
102. ust remain connected for most deployment scenarios Readable Writable Settings emn eoem ara samplwin Continuous periodic sampling false disable true enable window enable samstart Continuous periodic sampling yyyy mm dd hh mm ss window start time samstop Continuous periodic sampling yyyy mm dd hh mm ss window start time perdival Periodic sampling interval 1m 2m 5m 6m 10m 15m 20m 30m 1h 2h 3h 4h 6h 8h 12h 24h perdoffs Periodic sampling offset 0 to perdival in seconds Sample average size 1 100 114 118 SeaFET Manual Command Reference samdelay Sample delay s Time from wake up to start a sampling NOTE This setting is ignored if the external pump control is enabled logfrtyp Logged frame type NONE SHORT_ASCII FULL_ASCII Telemetry frame type NONE SHORT_ASCII FULL_ASCII logftype Log file generation rule ACQUISITION CONTINUOUS DAILY datfsize Size limit in MB for 0 255 0 No limit CONTINUOUS files msglevel Message log verbosity ERROR least verbose WARN INFO DEBUG most verbose msgtotlm Replicate messages in false disable true enable telemetry msgfsize Message file size limit KB 1 65535 thcal Thermistor calibration T0 T1 T2 T3 without any spaces constants inrefcal Internal reference calibration 10 11 without any spaces constants exrefcal External reference calibration E0O E1 without any spaces constants usepump false disable true enable pmpflush Flush time s T
103. wse 56 118 SeaFET Manual Deployment Deployment This chapter describes various deployment scenarios and how to configure and operate SeaFET for each Topics in this chapter include e Deployment Scenarios e Battery Endurance e SeaFET Deployment e Real Time Data Acquisition Acquisition Display e Logging Real Time Data Acquisition Monitor 57 118 SeaFET Manual Deployment SeaFET Deployment Scenarios Power Limited Applications Polled and Periodic operating modes are most convenient for power limited applications e g when SeaFET is being powered by the internal battery and or an auxiliary external battery Polled mode is used when SeaFET is integrated with an external master controller logger Periodic mode is ideal for autonomous operation Bandwidth Limited Applications If the application at hand is telemetry bandwidth limited and or the controller to with SeaFET is integrated has limited data storage capabilities configuration should involve the following Telemetry Settings Transmitted Frame Format SHORT_ASCII Instrument Logging Frame Format FULL_ASCII For all applications there is ample internal memory to accommodate high data volume internally It is therefore good practice to always ensure that both science and engineering data are stored by SeaFET internally FULL_ASCII If the application is not telemetry bandwidth limited and or the controller to which SeaFET is integ

SeaFET pH Sensor

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