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SUNACom User Manual

1. 79 82 SUNACom User Manual Performance Tuning Optimization for Temperature Salinity Correction Processing The calculation for temperate salinity correction depends on the processing algorithm for regular processing with some added overhead for the additional computations If problems exist and a more appropriate computer cannot be found SUNACom processing can be optimized by performance tuning the JVM described in the section below 80 82 SUNACom User Manual Performance Tuning Performance Tuning the JVM SUNACom is built using the Netbeans Platform and is tuned with the same mechanisms more advanced performing tuning options are explained here http performance netbeans org howto jvmswitches and http wiki netbeans org FaqNetbeansConf these options apply to all Netbeans based applications Processing larger or numerous files can be resource intensive If processing fails due to OutOfMemoryExceptions the application can be pre configured to use additional resources To do this edit the following file C Program Files x86 Satlantic SUNACom 3 0 0 etc sunacomsuite30 conf Modify the following switches in the default_options from J Xms24m J Xmx64m to J Xms512m J Xmx512m The 512m corresponds to he amount of RAM associated with the application In many situations for post processing increasing this value has the most impact on processing times Typically he more RAM that can associated with the process
2. Transition between Setup and Acquisition Transitioning between setup and data acquisition requires a few seconds for each direction A data acquisition cannot be started if insufficient power is supplied to SUNA The minimum requirement is a 8 15 VDC source supplying 1 A If insufficient power is supplied SUNA will shutdown and restart Erratic behaviour may result where SUNA repeatedly fails in its attempt to acquire data When SUNA is connected via USB only setup functions are available Data acquisition however requires an independent power supply Disconnecting SUNACom from SUNA while acquiring data is possible SUNACom will remind you that the SUNA is still collecting data if disconnecting in this state Unless you request that the data acquisition be terminated SUNA will continue its data acquisition until power is removed Connected with Data Acquisition During data acquisition SUNACom receives displays and optionally logs data transmitted by SUNA Ina laboratory setting SUNACom data acquisition provides a convenient method to analyze water samples When using SUNACom to prepare for a SUNA deployment data acquisition allows the operator to verify that the selected SUNA settings perform as intended 15 82 SUNACom User Manual SUNACom Overview Console Windows SUNACom records its actions and prints its command and data exchange with SUNA to three console windows Normally the console windows are displayed
3. Data Acquisition Display The Data Acquisition Display lets the you view or manage data that SUNACom receives from SUNA There are thee elements of the display e Real Time Data View lower left shows latest readings from selected sensors Graphs upper right display the values graphically Data Logging Window lower right for captuing streaming data in local files Normally all parts of Data Acquisition Display are opened when a data acquisition is started A display that was closed can be reopened via the SUNACom View menu SUNACom Preferences control which of the graphs appear at start up Real Time Data View The Real Time Data View prints the most recently measured SUNA data The display is located in the lower left part of the application window 25 82 SUNACom User Manual Running SUNACom i Real Time Display SUNA0167 Select Sensors Name Value Nitrate 0 16 ABS_254 0 03 ABS_350 0 03 Acquisition Information Acquisition Statistics SUNA0 167 Time Stamp 24 Sep 2012 16 14 06 UTC Frames Read 66 Lost Bytes 0 Fane Era 0 The real time data view Real Time Date View Configuration Initially only the nitrate concentration is shown Pressing the Select Sensors button opens the configuration dialog where the user can select other auxiliary sensors supply voltage internal humidity spectrometer temperature absorbance at 254 and 350 nm bromide trace
4. Running SUNACom The Output Field Delimiter is used to separate subsequent values in the file The separator can be acomma or a tab character When Output Extra Header Information is enabled an additional data row is generated at the beginning of the output file Using Satlantic Data Logger Time Stamps adds date and time values that were generated by a data logger to each measurement Usually this is not necessary because SUNA provides time stamps from its internal clock Selecting Output Frame Time Stamps adds the time stamps from the data frame to the output The Output Frames with Sensor Conversion Errors option removes any frame with a field that cannot be converted from the output Selecting Single Output File per Frame Definition will cause all output to be in one file Normally there is one output file for each input file Output Format options The Floating Point Conversion Type specifies if floating point values are written in decimal or scientific notation The Floating Point Precision specifies the number of significant digits in a floating point number Suppress Non numerical Output Values to omit text content from the output file Hexadecimal Output Values can only be used when the Calibrated Sensor Values option is disabled Then integer values are output in hexadecimal format With the Format Frame Time Stamps option time stamps in printed in human readable format as opposed to a format more suited for softwar
5. reference spectrum g Compare new reference spectrum to current wizard 3 of 4 Percent Change in Reference Spectra 15 0 D a125 10 0 Vv 2 75 5 0 B E a D 25 00 omassaan 200 225 250 275 300 325 350 wavelength nm E difference from SNAO167M CA lt Back Next gt Finish Cancel Help Reference Update Dialog Compare new and previous spectrum Step 4 Upload the new reference spectrum The new reference spectrum is joined with the extinction coefficients of the currently active calibration file to generate a new calibration file That new calibration file will be loaded onto SUNA At the same time that calibration file is copied to a user selected location on the computer A report file of the update containing a spectrum plot a relative change plot and an optional comment is generated in PDF format and also copied to the user selected location 46 82 SUNACom User Manual Running SUNACom P Calibration Wizard Ss Steps Upload calibration file with new reference spectrum wizard 4 of 4 1 Fill the sampling volume with DIW Local Filesystem 2 Acquiring spectra data from SUNA Output Directory C Users SUNA data 3 Compare new reference spectrum to current F Overwrite Existing Calibration File 4 Upload calibration file with new reference spectrum f Report File Name SNA0167N pdf View Report Comment
6. 0 025 0 000 0 025 0 050 0 075 0 100 Absorbance 0 125 0 150 0 175 0 200 aS eee ns 0 225 0 250 0 275 210 220 230 240 250 260 270 280 200 300 310 320 330 340 350 360 370 380 Absorbance Counts 0 The absorbance graph Absorbance Graph Configuration The Total Absorbance graph can be configured by pressing its Configure button The Configure Graph dialog is displayed to allow the minimum wavelength for total absorbance that will be plotted to be specified The option to have its graph history to be either unbounded or to be limited to a specified number of graphs When the graph history is limited to a specified number the slider will only allow this number of the most recent Total Absorbance graphs to be viewed f Configure Graph Min Wavelength Cutoff 210 gt nm Graph History Unbounded Graph History Limit 1 7 The absorbance configuration dialog Zooming on the Total Absorbance Graph Zooming in and out of the Total Absorbance Graph can 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 31 82 SUNACom User Manual Running SUNACom left mouse button down zooms the graph back out The zoom functions are also available on a
7. As an admin user re execute the the script Library Application Support SUNACom2 2 postinstall This should set the permissions for normal operation 74 82 SUNACom User Manual Troubleshooting SUNA Performance Issue SUNA Self Test Whenever a SUNA is acting in an unexpected way it is a good idea to run the self test function to ensure the hardware is functioning properly If any unexpected results occur please contact Satlantic support for assistance 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 SUNACom Error Event panel should be displayed in the SUNACom GUI SUNACom is built in a way that will display this frame corruption to the user then ignore these corrupt data points and continue SUNACom Application Logs All activity that occurs with SUNACom 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 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 i
8. Driver Check System Profiler under Application Utilities to ensure the USB to Serial adapter is installed It should show up in the available list of USB devices 71 82 SUNACom User Manual Troubleshooting QOO Mac mini aluminum macmini 2 15 11 12 49 PM Contents Y Hardware Vv USB Bus ATA Audio Built In Y BRCM2070 Hub Bluetooth Bluetooth USB Host Controller Card Reader IR Receiver Diagnostics Vv USB Bus Disc Burning USB Optical Mouse Ethernet Cards USB High Speed Bus Fibre Channel Y USB High Speed Bus FireWire VW Keyboard Hub Graphics Displays Apple Keyboard Hardware RAID UC232R Memory e PCI Cards Product ID 0x6001 Parallel SCSI Vendor ID 0x0403 Future Technology Devices International Power Limited Printers Si mies FTF7G29F SAS Speed Up to 12 Mb sec Serial ATA Manufacturer FTDI USB Location ID 0x06200000 YW Network Current Available mA 500 AirPort Current Required mA 100 Firewall Locations Modems Volumes v Using a working USB to Serial adapter continue troubleshooting as in the case where the serial cable is connected to a serial port Using a Serial Cable with a Serial Port It is possible that the failure to connect is related to SUNACom To find out connect using a terminal emulator e When running Windows use e g HyperTerm or TeraTerm en sourceforge jp projects ttssh2 releases e When running Mac OS X use e g iTerm http iterm sourceforge net downloads s
9. a record of the number of measurements that were received e The Acquisition Monitor keeps track of possible errors in the transfer during data acquisition 67 82 SUNACom User Manual Running SUNACom SUNACom Window Menu The SUNACom window menu accesses functions that affect the running of the SUNACom application without impact on the connected sensor The following functions are available Maximize Window will fill the SUNACom window with the currently active sub window e Close Window will close the currently active sub window Undock Dock Window will make the currently active sub window freely movable on the desktop e Close all Documents will close the sub windows with the exception of the SUNACom Dashboard e Reset Windows will open close and arrange sub windows as they are when the SUNACom application is started 68 82 SUNACom User Manual Running SUNACom SUNACom Help Menu The SUNACom help menu collects tools to assist in operating SUNACom The following functions are available Help Contents for accessing interactive help for SUNACom operation e Troubleshooting for guidance through problems when running SUNACom or when interacting with SUNA e Satlantic for opening Satlantic s website in a web browser e User Manual for viewing this manual About displays Satlantic contact information and the version of SUNACom that is running 69 82 SUNACom User Manual Troubleshoot
10. check by first cleaning the windows and waiting until the isopropyl alcohol has completely evaporated Then the sampling volume is filled with ultra pure DIW and data are acquired ideally replicating conditions of the past or planned deployment Both the time sequence and the external temperature should match the deployment conditions as closely as possible For example if the deployment is on a moored platform in arctic waters and the data acquisition occurs in short bursts the reality check should collect a short burst of data from a SUNA places in chilled water On the other hand if the deployment collects long time profiles SUNA should run over a period of at least 10 minutes to stabilize the internal temperature before conducting the reality check SUNA accuracy specifications depend on the optical path length 10 mm or 5 mm and on the calibration type fresh water or seawater If the reality check gives a nitrate concentration that is outside the specification the reference spectrum should be updated Deployment Considerations For best data quality the SUNA nitrate concentration of a DIW sample should be reality checked before and after a deployment and if possible also when it is serviced during deployments When a SUNA is recovered an initial reality check without first cleaning the windows is useful This initial check measures the total drift over the deployment duration Then a second reality check is done after the window
11. configured in many ways Configure Graph The time axis of the graphs is either limited or unbound During a data acquisition a time limited axis means that only the most recent data will be plotted when replaying logged data a time limited axis displays the latest subset of data points z t Configure Graph l Time Axis Range Unbounded Time Axis Range Limit 5 gt min EE Zoom and Auto Range Buttons Zooming into and out of the Time Series Graph can be accomplished by using 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 centre 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 changes 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 Zoom using the Mouse 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
12. menu that pops up when the right mouse button is clicked over the graph Data Logging Window 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 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 automatically stops when the acquisition is stopped Data Logging Frames Logged 0 Log Timer O StartLog Logging Options Log File Prefix SUNA Log Directory C Data SUNACom Browse Previous Log File s Auto Logging Auto Log Duration 00 00 00 Repeat Auto Log after Interval 00 00 00 The data logging panel Data Acquisition Monitor The data acquisition monitor displays data acquisition statistics The monitor keeps track of the number of data frames that SUNACom receives from SUNA and identifies errors occurring within those frames The counters in th
13. nitrate concentration into a voltage and a current The nitrate range specifies the nitrate concentrations corresponding to the low and high voltage and current output The nitrate range should match the expected measurement range Selecting a too narrow range can cause loss of information a too wide range reduces the resolution When the nitrate range is changed a DAC Calibration will be required The adaptive integration time capability allows SUNA to operate in optically dense environments This feature is crucial to ensure operation in a wide range of water conditions If adaptive integration is turned on SUNA evaluates the current water transmittance At low transmittance it increases the integration time to obtain a sufficient measurement signal even in optically dense conditions A side effect of the inceased integration time is that the data rate decreases Typically water that requires the use of an increased integration time has high levels of turbidity suspended matter tnd may additionally have high levels of CDOM coloured dissolved organic matter The adaptive integration algorithm continuously monitors the transmittance and switches back to the normal integration time when contions permit When the persistent option is checked the very first measurement after a power cycle will use the integration time that was in use at the end of the previous measurement event After that very first measurement automatic adjustment will continue to
14. operate SUNA calibrations can be done for fresh water or seawater Sensors with a seawater calibration file can be used in either type of water A fresh water calibration file will produce incorrect results in seawater The Seawater Calibration panel is shown if the currently active calibration file is suitable for seawater When the planned deployment will be in fresh water the deployed in fresh water option should be selected for improved accuracy and precision of the measured nitrate concentrations Fresh Water Calibration v Bromide Trace The Fresh Water Calibration panel is shown if the currently active calibration file is suitable for fresh water A Bromide Trace can be measured in freshwater only Thus it is available when selecting deployed in fresh water in seawater calibrations and always in fresh water calibrations Tracing Bromide reduces accuracy and precision of the nitrate concentration Use it only when needed SUNA File Manager The File Transfer dialog SUNA has internal memory to store calibration files and an optional file system for data and message logging The file transfer 40 82 SUNACom User Manual Running SUNACom Calibration file management is crucial for data quality A specific calibration file is valid for a certain time period after which it may be replaced by a calibration file containing a more recent reference spectrum When reprocessing or interpreting data it is crucial to use the app
15. the Sensor menu SUNA Settings General Telemetry Advanced A CAUTION Modifying advanced settings can adversely affect SUNA performance Fitting Range 217 0 gt 240 0 nm Integration Period 250 msec Nitrate DAC Nitrate Units mg l Nitrate Range 0 07 gt 1 40 uM Adaptive Integration On Off Persistent Salt Water Calibration Deployed in Fresh Water Bromide Trace peed canes eta Cu The fitting range defines the wavelength interval that is used when calculating the nitrate concentration The normal range of 217 240 nm is well suited for operation in fresh water and seawater Adjustment of the interval is only advisable if the water sample contains substances that exhibit strong absorbance in that interval interfering with the normal calculation In such a situation and after consultation with Satlantic it may be useful to slightly adjust the fitting range 39 82 SUNACom User Manual Running SUNACom The integration period specifies the SUNA spectrometer integration time in milliseconds It is selected at Satlantic for optimal SUNA performance and must match the integration period used during calibration If the SUNA lamp intensity were to drop significantly for compensation the integration period could be increased In such a situation and a reference update must also be performed SUNA has an optional Digital to Analog Converter DAC transforming the measured
16. the Serial Interface Frame Format Integrated Wiper If present the integrated wiper operation can be enabled or disabled Wiper Settings Integrated Wiper Enabled SUNA Messages During opertion SUNA sends status messages to serial or USB output If the SUNA file system is present these messages are also logged to the SYSLOG LOG file Use the logging level drop down box to select the desired message sensitivity The log levels are cumulative i e if selecting INFO then WARN and ERROR messages are also generated TRACE The most detailed level of logging should only be used by support for troubleshooting Operating at this level will slow down SUNA operation DEBUG Detailed messages are generated which are useful for troubleshooting problems INFO Typical log level for interactive use and deployment generates startup and shutdown messages WARN Generates only warning messages suitable for long deployments e ERROR Error messages typically require investigation and user intervention The maximum log file size limits the amount of messages that are kept When the maximum size is reached SYSLOG LOG is copied to SYSOLD LOG any prior log file is deleted and a new SYSLOG LOG file is started SUNA Telemetry Settings Data Transmission SUNA communicates over its serial interface at a user selectable baud rate Supported values are 9600 19200 38400 57600 and 115200 During data acquisition measurement res
17. the better up to the 80 90 of the physical ram installed on the computer Also setting the ms value to the mx usually helps 81 82 Index A U Upload Firmware 52 Upload Instrument Files 53 Acquisition 24 V Acquisition Display 25 Acquisition Monitor 32 Application Log 20 w View Menu 67 B Window Menu 68 Binary Convert 61 C Calibration Update 42 Command Terminal 48 Compare Calibration 65 Console Windows 16 Convert APF Data 64 Create Report 48 D DAC Calibration 51 Dashboard 13 Data Logging Headers 49 H Help Menu 69 l Installing 8 O Overview 11 P PerformanceTuning 77 Q QuickStart 5 R Replay Logged Data 60 S SUNA Advanced Settings 39 SUNACom Preferences 18 SUNACom Tools 54 SUNA General Settings 34 SUNA Self Test 50 SUNA Serial Connect 22 SUNA Settings 33 SUNA Telemetry Settings 37 Sync SUNA Time 47 T Troubleshooting 70 82 82
18. 0361 C5 Converted Data Files Output Directory F itemp OK Cancel Help Compare Calibration The calibration file comparison plots the relative change of the reference spectrum between two calibration files Over time the optical components of a SUNA drift slightly causing a bias in the measured nitrate concentrations A reference update generates a new calibration file with an updated reference spectrum Only the reference spectrum in the new calibration file is modified The wavelength column and the extinction coefficients of the calibration file describing intrinsic properties of the spectrometer and of chemical species are not changed The comparison function shows the spectral basis of the SUNA drift The calibration file comparison is accessed via the SUNACom Data menu It is also automatically preformed as part of the Update Calibration procedure When executed a dialog for entering the two calibration files opens The plot of the relative change is shown in the dialog The magnitude of the change between two reference spectra updates depends on how much time passed between the updates and the amount of lamp use during that time Typical update intervals of 3 6 month with no more than 100 lamp use hours in between should cause a change of no more than 10 in the 215 240 nm interval which is the wavelength range used for nitrate processing At wavelength below 215 nm larger relative changes can b
19. 1016 9 Spec Lght av sd mi ma 23285 12372 1051 52083 10 Ok 50 82 SUNACom User Manual Running SUNACom Each line is the test result for one specific system if the performance is outside the accepted range that output line is terminated by an exclamation mark and the self test will report an error on the last line 10 Log data file system total size and remaining size The logging file system is optional Internal file system total size and remaining size The internal file system is used internally its failure would compromise SUNA operation Cumulative lamp run time The total expected life time of the lamp is 900 hours Temperature sensors internal housing spectrometer and lamp The temperatures should be close to ambient temperature if the sensor was recently operating temperatures may be higher Internal relative humidity in percent If the internal humidity exceeds 10 the sensor may have a leak Voltages and current The main supply board and processor voltages should be in the 8 15 11 5 12 5 and 4 75 5 25 V ranges respectively the total current is expected to be below 100 mA Lamp power consumption The nominal power consumption is 7500 mW Spectrometer dark measurement reporting average standard deviation and minimum to maximum range The dark spectrum average should be in the 500 1000 count range and the standard deviation should not exceed 12 counts S
20. 11 10 09208 07 12 3 34 567 An icon will show when the data have been loaded If the SUNA and TS data clocks were not synchronized a time offset can correct this A Temperature amp Salinity Correction v Activate Temperature amp Salinity Correction Sakamoto et al 2009 CTD Data From SUNA APF Mode Frames Data From External File External File C Users SUNA datal TankLog 2012 08 15 csv Browse Data Loaded Time Offset sec 00000 The temperature salinity correction panel The processing results can be written to file or viewed in a graph e When writing to file the default output directory as specified in the SUNACom Preferences can be overwritten e When processing multiple files the results can be directed into a single output file otherwise there will be one output file for each input file An optional graph of the results is shown in the view area of the SUNACom window The upper graph shows how the chemical species combine to achieve the measured absorbance A Below that is a time line of the original and reprocessed nitrate concentrations The slider underneath the time line selects one measurement the concentration of which is shown to the left and the associated absorbance decomposition is plotted at the top A second panel shows the absorbance curves for all measurements 57 82 SUNACom User Manual Running SUNACom Reprocessed Nitrate Graph 38 Ae Configure a Absorption Comp
21. ACom The logging level is selected via a drop down box The log levels specifies the type of messaged to be logged Log levels are inclusive e g at the INFO level also WARN and ERROR messages are recorded The following levels can be selected e TRACE The most detailed logging generates very large log files and should only be used for troubleshooting e DEBUG A high level logging used for troubleshooting problems e INFO The typical level of logging collects all high level operations e WARN This reduced level of logging eliminates the possibility of using the log files as a means to record SUNA configuration and use e ERROR At the minimal logging level only errors that require investigation and user intervention are recorded When the Display Dialog for Error level Messages option is checked SUNACom will open a dialog when an error occurs Such an alert desirable since errors are unexpected and need to be investigated There is a choice between Daily and Rolling Log Files In the first case all messages generated during a single day are written to one file In the second case messages are written to file until the file reaches a specified size limit Then message writing is rolled over to a new file A maximum number of those files will be kept with the oldest files deleted first If the Enable Logging Lost Bytes option is checked SUNACom writes all unexpected SUNA output it receives during a data acquisition to f
22. CII format ie sensor headers extra header info tab delimiter etc The Convert Raw Data function is accessed via the SUNACom Data menu A dialog will open requesting the following input The instrument package file specifies the input binary frame format The instrument package file can be found in the Calibration files folder SUNACom install disk or in the default application folder on your computer Windows XP C Documents and Settings USERNAME My Documents Satlantic SUNA Windows Vista Windows 7 C Users USERNAMES My Documents Satlantic SUNA 61 82 SUNACom User Manual Running SUNACom Mac OS X Users Home Satlantic SUNA e The tree selector specifies the sensors to be included in the conversion The raw data files contain the binary data that are to be converted e The options for the converted data files control the file and data format See below for a detailed description e The output directory for the converted data files will contain the SUNACom generated output files C Temp SUNA_0095_001 xml sunaooss A a M E V CHECK HUMIDITY LAMP_TIME NITRATE_MG NITRATE_UM RMSe SPEC_AVG TIME T_LAMP T_SPEC m ISISSSSSSS C Pata SUNA 0095_2010 11 24_15 32 03_raw bin Converted Data Files C Data Converted Output Directory Conversion Type options 62 82 SUNACom User Manual
23. Calibration File Name SNAO167N cal View Status The new calibration file will be saved in the selected local directory lt Back Next gt Finish Cancel Help Reference Update Dialog Upload new reference spectrum Set SUNA Clock Set Clock synchronizes the SUNA internal battery backed clock to the computer clock The internal clock has an accuracy of 60 seconds per year and operates in UTC Coordinated Universal Time This function is provided to correct either small accumulated inaccuracies or incorrectly set times The Set Clock function is available via SUNACom s Sensor menu The dialog displays the running time of both the computer and SUNA Both times are displayed either in UTC or in local time depending on the user selected Use UTC Time preference which can be set by the SUNACom Preferences dialog When pressing the Sync Time button SUNACom synchronizes the SUNA clock to the computer clock An accurate SUNA clock time requires a computer clock that has previously been synchronized to a standard clock The synchronization is accurate to at least 2 seconds 47 82 SUNACom User Manual Running SUNACom r Set Clock Instrument Time 30 Nov 2011 16 27 41 UTC Computer Time 30 Nov 2011 16 27 43 UTC Sync Time Cancel Help Image Caption The Set Clock dialog Summary Report A summary report is a PDF file that contains the current SUNA settings It offers a co
24. Display To stop data replaying press the Stop button on the SUNACom dashboard 60 82 SUNACom User Manual Running SUNACom K 3 Replay Logged Data x Steps Replay Logged Data 1 Replay Logged Data Instrument Package File C Users SUNA Documents SUNA_0095_001 xml Browse SUNA Raw Data File C Users SUNA Documents SUNA 0095_2010 11 24_raw bin Browse J Display Total Absorbance SUNA Calibration File C Users SUNA Documents SNA0095B CAL l Browse Status All fields validated Press Finish to Start Acquisition lt Back Next gt Finish Cancel Help The replay logged data panel Raw Data Conversion SUNA generates data in a number of frame formats among them Full_Binary and Reduced _Binary Binary data formats are more compact than the equivalent ASCII data format leading to reduced storage space and transmission times However whereas ASCII formats are human readable and easily used in applications like spreadsheet programs binary data require special applications for data analysis SUNACom offers binary to ASCII conversion to facilitate analysis of data that were acquired in binary format SUNA can also generates data in ASCII frame formats among them Full _ASCII and Concentration These ASCII data formats do not contain any sensor values that can be converted from raw to fitted values but converting data frames in these formats can provide other useful features of the converted AS
25. Fitting errors cannot occur for SUNA frames Data Acquisition Monitor FRx SATSLFOO95 CheckSum Errors Counter Errors Status Errors Fittting Errors SATSLCO095 SATSDCO095 SATSDF0095 SATSDB0095 SATSLB0095 SATSDRO095 SATSLRO095 o o o o o ol oo o o o o o o oo o o o o o o olo Oo o o o o o olo Oo0 o0 o0 o0 oIoIo o o o o m o o o SUNA Settings SUNA settings determine how SUNA operates during a data acquisition These settings are conceptually grouped into Factory Settings describing the SUNA hardware and build configuration they cannot be modified and SUNACom adjusts its user interface based on the features supported by the SUNA Communication Settings determine how SUNA interfaces with its controller e g SUNACom Data Acquisition Settings define how SUNA operates whenever power is applied Data Processing Settings specify how each spectral measurement is transformed into a nitrate concentration SUNACom displays the current SUNA settings in a panel that is organized into three tabs 33 82 SUNACom User Manual Running SUNACom e The General Settings Tab presents data acquisition parameters relevant to the selected operating mode e The Telemetry Settings Tab contains settings relevant to I O and internal data logging e The Advanced Settings Tab provides options on data processing and analog output if available in hardware Ch
26. Humidity Voltage Internal Temperature V Absorbance at 254nm v Absorbance at 350nm Bromide Trace JCcne Hp The real time data view sensor selection Time Series Graph The Time Series graph plots the nitrate concentration and any selected optional values against time The display is located in the upper right part of the application window in a tabbed pane The time series graph offers a convenient way to monitor data during a data acquisition It is also used when replaying logged data 26 82 SUNACom User Manual Running SUNACom Time Series SUNAO167 LD Gzoomm Q Zoomout Auto Range Time Axis Range Axis Time Series Select Sensors Configure 16 13 00 16 13 10 16 13 20 16 13 30 Time UTC Nitrate ABS_254 ABS_350 16 13 50 16 14 00 The time series graph Time Series Graph Configuration The Select Sensors button allows the addition of data to or removal of data from the time series graph When the selection is changed during a data acquisition the plots are restarted at the current time Internal Temperature V Absorbance at 254nm V Absorbance at 350nm Bromide Trace Ces Lie The time series sensor selection 27 82 SUNACom User Manual Running SUNACom The plot range can be
27. SATLANTIC SUNA SUNACom Manual 3 0 11 SAT DN 00498 3 0 11 551 2015 04 17 03 22 Copyright 2012 Satlantic All rights reserved Table of Contents Quick Start Guide 5 Installing SUNACom 8 Overview 11 Dashboard 13 Console Windows 16 Running SUNACom 17 SUNACom Menu 18 Preferences 18 General 18 Display 19 Message Logging 20 Sensor Menu 22 Connect to Instrument 22 Acquisition 24 Acquisition Display 25 Acquisition Monitor 32 SUNA Settings 33 SUNA General Settings 34 SUNA Telemetry Settings 37 SUNA Advanced Seitings 39 Transfer Files 40 Calibration Update 42 Set Clock 47 Summary Report 48 Advanced Functions 48 Command Terminal 48 Edit Log Headers 49 SUNA Self Test 50 DAC Calibration 51 Upload Firmware 52 Adminsitrative Settings 53 Data Menu 54 Reprocess Data 54 Replay Logged Data 60 Convert Raw Data Files 61 Convert APF Data 64 Compare Calibrations 65 View Menu 67 Window Menu 68 Help Menu 69 Troubleshooting 70 Performance Tuning 77 Index 82 SUNACom User Manual Quick Start Quick Start 5 82 SUNACom User Manual Quick Start Installation and Setup Install SUNACom software and connect to SUNA 1 The SUNACom installer is available at Satlantic s website http www satlantic com Download the executable for your operating system 2 Run the downloaded installer See Installing SUNACom for details and requirements 3 Start SUNACom On a MS Windows syst
28. SUNA calibration in the field and in the lab e Display of data in real time e Logging and reprocessing of data e Management of SUNA internally logged data The SUNACom window normally displays three areas the content of which changes depending on SUNA operation and operator actions e The Communication Dashboard offers access to frequently used functions and gives basic information about a connected SUNA These functions are also available through the Sensor menu and via the tool bar The dashboard area is reused for Reprocessing Data a function only available when SUNACom is disconnected from SUNA The main view is by default the largest area within the application Because of its larger size it is where graphs and files are initially shown The output area is located along the bottom of the application Components placed in this area are those usually best viewed horizontally Typically it will contain output of log files along with smaller UI Components that can be show in a condensed space 11 82 SUNACom User Manual SUNACom Overview Dashboard Main view Console SUNACom Window Layout 12 82 SUNACom User Manual SUNACom Overview SUNACom Dashboard The dashboard is the starting point for interacting with SUNA At start up SUNACom is disconnected from SUNA After the SUNA cables are connected initiate the connection by pressing the connect button SUNACom establishes the connection and enters the setup s
29. ader lines as well as the values of all headers can be freely edited When the Prompt option is checked the dialog opens whenever a new data log file is started This allows for an easy input of per file header values which can be useful when SUNA is used to analyse multiple distinct samples 49 82 SUNACom User Manual Running SUNACom i Data Logging Headers x Manual Value Headers Name Value Add OPERATOR user name EXPERIMENT Remove COMMENT V Prompt Data log file headers dialog SUNA Self Test The SUNA Self Test executes a series of internal tests These tests internally check the function of all main SUNA components The self test verifies that all systems of the sensor are functional and gives an Ok or an Error result The self test should be executed when a problem is suspected The output generated during the test allows the operator or Satlantic support to identify the cause of a problem The Self Test is executed from the Advanced submenu in SUNACom s Sensor menu The output of the self test consists of some ten lines that will resemble the following example 1 Extrn Disk Size Free 1960968192 1871413248 2 Intrn Disk Size Free 2043904 1998848 3 Fiberlite Odometer 0001 32 59 4 Temperatures Hs Sp Lm 22 4 21 6 23 0 5 Humidity 39 5 6 Electrical Mn Bd Pr C 13 9 11 9 5 1 25 4 7 Lamp Power 7195 mW 8 Spec Dark av sd mi ma 993 10 964
30. ames Sample Averaging Number of Measurements per Frame 1 Deployment Characteristics Estimated Frame Rate 1 0544 frames sec Wiper Settings Integrated Wiper Enabled SUNA Messages Logging Level INFO a Maximum Log File Size 2 gt MB Ce eta He Continuous Mode In continuous mode SUNA begins acquiring data when powered up and stops when power is removed An acquisition consists of an initial dark sample followed by a cycle of light and dark measurements A periodic dark measurement improves the accuracy of the nitrate concentrations especially if the sensor temperature is fluctuating The frequency of the dark measurement is controlled either by the number of alternating dark and light frames or by the dark and light duration Fixed Time Mode Fixed time mode is almost identical to Continuous mode The only difference is that the instrument stops acquiring data after a user configurable period Acquisition Time in Fixed Mode and enters low power sleep 35 82 SUNACom User Manual Running SUNACom E amp SUNA Settings General Telemetry Advanced Operational Mode Fixed Time Mode Settings Fixed Acquisition Time 60 sec gt Frame Based Operation Time Based Operation Frame Cycle 120 seconds of light frames 10 seconds of dark frames Periodic Mode In periodic mode acquisition events are uniformly distributed over a 24 hour day as spec
31. anges made on these tabs are applied to SUNA when the Upload button is hit SUNA General Settings SUNA data acquisition is primarily controlled by the operating mode and then fine tuned by additional settings Continuous SUNA continuously and indefinitely acquires data Fixed time SUNA acquire data for a duration specified by the operator Periodic SUNA periodically acquires a brief burst of data e Polled SUNA acquires data when receiving commands e APEX Float SUNA acquires data when commanded via the APEX float controller protocol e SDI 12 SUNA acquires data when prompted by a SDI 12 controller Settings for fine tuning of each operating mode are shown when selecting that specific operating mode These and references for command or controller driven operation are discussed below SUNA can operate autonomously in Continuous Fixed Time and Periodic mode These three operting modes are supported in SUNACom SUNA can also respond to commands by a controller when in Polled APEX Float or SDI 12 mode SUNACom cannot serve as a controller in these operating modes The interfaces for these modes are defined in separate sections in the user manual 34 82 SUNACom User Manual Running SUNACom SUNA Settings a General Telemetry Advanced Operational Mode Continuous X Continuous Operational Mode Settings 5 Frame Based Operation F Frame Cycle 120 seconds of light Frames 10 seconds of dark fr
32. as tabs in the output window located in the lower right of the SUNACom application window They can however be closed and reopened via the Output sub menu in SUNACom s View menu The Application Console logs the SUNACom activity For future reference these messages are also written to file Besides providing a record of SUNA interaction including setup and data acquisition this record also captures warning and error messages Troubleshooting can be facilitated by having access to a complete log of the SUNACom to SUNA interaction The Setup Console displays the commands sent to SUNA and the responses received by SUNACom while in setup mode The command exchange is not recorded to file However the application console log records the commands sent to SUNA The Acquisition Console displays the data frames that are received by SUNACom while SUNA acquires data While SUNACom runs a data acquisition these data frames can be saved to file via the data logging window 16 82 SUNACom User Manual Running SUNACom Running SUNACom The SUNACom menu bar gives access all program functions Some of those functions are also available via the tool bar directly below the menu bar other functions are accessible via the dashboard The SUNACom menu for configuring the SUNACom application e The Sensor menu for interacting with SUNA The Data menu for handling data acquired by SUNA e The View menu for enabling or disabling panels displa
33. ctPort java 155 java lang Thread run Thread java 619 Stack trace messages help Satlantic support to diagnose errors When reporting an error to Satlantic please include The SUNA serial number and firmware version see SUNACom Dashboard The SUNACom version you are using see SUNACom About dialog SUNA logged data file SUNACom message log file 76 82 SUNACom User Manual Performance Tuning Performance Tuning In its standard configuration SUNACom is optimized for SUNA setup and short data acquisition sessions on computers that meet or exceed the minimum software requirements This section explains how to optimize performance for processor intensive operations 77 82 SUNACom User Manual Performance Tuning Optimization for Data Logging During data logging the display of data in real time uses most of the processor resources See SUNACom preferences for custom setup If a particular view is required and cannot be removed i e time series absorbance or spectrum its operation can be optimized to increase its particular performance by editing its display settings The available settings for each view will can be shown by clicking on the settings button in the upper right hand corner of each view Of particular importance for performance is the number of elements in the absorbance and spectrum sliders and number of points within the time series view If performance problems still exist consider performanc
34. e When Display Converted Data is checked the output data are printed in the SUNACom view area Error Checking options The Frame Counter if present in the input frame should increase by a value of one from frame to frame Any unexpected jumps will be logged to the Application Console in the Output Window The Check Sum if present in the frame will be checked for each frame If valid the converted frame will have a zero entry for hte checksum field If invalid the frame is not converted 63 82 SUNACom User Manual Running SUNACom iG gt Conversion Options X Conversion Type Output Format Output Field Delimiter Floating Point Conversion Type Decimal X Floating Point Precision 1 Output Extra Header Information Suppress Non numerical Output Yalues Use Satlantic Data Logger Time Stamps Hexidecimal Output Values v Output Frame Time Stamps k Format Frame Time Stamps Output Frames with Sensor Conversion Errors R f a Display Converted Data Single Output File per Frame Definition Error Checking 7 Frame Counter if available J Check Sum if available La Col a APF Data Conversion SUNA generates data in a number of frame formats among them ASCII formatted APF frame It provides a compact data representation for applications that cannot easily utilize binary data However whereas other ASCII frame formats are human readable and easily used in standard applicatio
35. e SUNA settings to a PDF file Advanced Functions o Command Terminal sends commands directly to the SUNA command line o Edit Log Headers o SUNA Self Test verifies that the sensor is properly functioning o DAC Calibration aids in generating calibration coefficients for SUNA analog output o Upload Firmware installs a new firmware on SUNA o Administrative Settings o Upload Instrument XML File Connecting to SUNA SUNA connects via either RS 232 serial or USB to the computer When using the RS 232 serial connection SUNA also requires 8 15 VDC power providing at least 1 A The USB connection provides sufficient power for communication but in order acquire data additional 8 15 VDC is required 22 82 SUNACom User Manual Running SUNACom The SUNA default configuration ensures that the sensor enters autonomous data acquisition whenever it is powered However this default setting may be not optimal for a given deployment and adjusting the setting may provide better results Running a test data acquisition in SUNACom will confirm that the selected settings give the intended performance When connected via USB the SUNA initiates a virtual serial port communication As a consequence both the RS 232 and the USB connections appear to the computer as serial connections Usually RS 232 ports have small one digit numbers and USB virtual ports have larger sometimes two digit numbers To initiate communication from SUNACom to
36. e expected At wavelength above 240 nm the change is normally smaller than in the 215 240 nm interval In case of a large unexplained change the stability of the reference spectrum should be monitored by performing a few reference updates some 12 24 hours apart If changes in the reference spectra persist contact Satlantic for support 65 82 SUNACom User Manual Running SUNACom Select First Calibration File C Users SUNA Documents SNA01494 cal Browse se Select Second Calibration File C Users SUNA Documents SNA0149B cal wse Calibration instrument serial numbers match Percent Change in Reference Spectra Fa ul Fa M in 1Y N in w 2 20 0 v 200 225 250 275 300 325 350 wavelength nm The calibration file comparison dialog 66 82 SUNACom User Manual Running SUNACom SUNACom View Menu The SUNACom view menu accesses functions that affect the running of the SUNACom application without impact on the connected sensor The following graphical or text windows are available e Under Graphs the Spectra Graph the Time Series Graph the Absorbance Graph or the Reprocessed Nitrate Graph are accessed Under Output the Setup Console the Acquisition Console the Reprocessing Console or the SUNACom Application Console are accessed e The Real time Data view displays the latest sensor values when acquiring SUNA data e The Data Logging view keeps
37. e monitor are reset when a new data acquisition is started and are updated in real time Data acquisition errors should not happen However they can occur in the sensor or during data transmission SUNACom notices such errors and displays that information in the data acquisition monitor Below error types are explained and troubleshooting steps are identified The data acquisition monitor is opened in two steps First open the Real Time Data display via SUNACom s View menu There under Acquisition Information press the Error Details button to access the Data Acquisition Monitor 32 82 SUNACom User Manual Running SUNACom The monitor tracks the following fields Frame Id The unique identifier of a frame Frames are defined in the instrument package file Read The number of frames accepted during the current acquisition Errors The number of frames discarded during the current acquisition Checksum Errors The number of frames with a checksum error Some values in such a frame are wrong therefore the frame is discarded Checksum errors indicate a data transmission problem The cable and the connectors should be checked If SUNA internal data logging is used the correct data will be in internal memory and can be downloaded at a later time Counter Errors Always zero Counter errors cannot occur for SUNA frames Status Errors Always zero Status errors cannot occur for SUNA frames Fitting Errors Always zero
38. e through the View menu The commmand terminal is available via the Command Terminal entry in the Advanced sub menu in the SUNACom Sensor menu An alternative to the SUNACom command terminal is a terminal emulator HyperTerm TeraTerm iTerm To use a terminal emulator first disconnect from SUNACom then reconnect to the terminal emulator Data Log File Header SUNACom can serve as a data logger when controlling a SUNA data acquisition Data files logged by SUNACom contain the data frames sent over telemetry plus a file header The data log file header provide a means for attaching meta data to a data file The header lines are of the form SATFHR Header Identifier Header Value The following example shows a header containing for default header lines followed by four user defined header lines SATFHR FILE VERSION 3 0 0 SATFHR APP VERSION SUNACom 3 0 3 SATFHR INSTR PACKAGE SUNA_0166_001 xm1 SUNA0166 1 0 2011 11 28 0400 47230 SATFHR TIME STAMP 2012 12 19T12 45 29 0400 SATFHR OPERATOR Robin Smith SATFHR EXPERIMENT Lake Water Analysis SATFHR COMMENT Samples After Rainstorm SATFHR LOCATION Nutrient laboratory Access the Edit Log Headers dialog from the Advanced sub menu in the Sensor menu The dialog always lists the OPERATOR EXPERIMENT and COMMENT headers Additional header lines can be created or deleted via the Add and Remove buttons The names of the added he
39. e tuning the JVM described in the section below 78 82 SUNACom User Manual Performance Tuning Optimization for Data Reprocessing Reprocessing large amounts of data can be time consuming we recommend a computer that significantly exceeds the minimum requirements the amount by which you should exceed the minimum requirements depends on the re processing job To judge the processing load for a batch processing job we recommend first processing a single file and monitoring system performance while processing This should give a good indication on how a larger batch job will perform Within the application performance can be increased by 1 Closing all other applications freeing up resources for processing 2 Using batch mode which does not output to graphs 3 Outputting each result to its own file uses less resources 4 Minimizing the SUNACom application while processing can free up a little more resources for processing 5 Using the Shift key to select subsets of files to batch process rather than processing them all at once Processing performance is impacted by 1 Data files size number of frames per file 2 Number of data files to be processed in batch mode 3 Situations where the Nitrate value is high 4 Corrupt data frames or sensors values If problems exist and a more appropriate computer cannot be found SUNACom processing can be optimized by performance tuning the JVM described in the section below
40. eived by SUNACom Data acquisition terminates when the operator stops the data acquisition or if SUNA power is removed Fixed Time SUNACom opens a dialog showing the duration of the fixed time data acquisition After confirmation SUNACom passes control to SUNA which autonomously acquires data for the configured duration The data stream will be received by SUNACom In order to return to setup mode press the Stop button on the SUNACom dashboard Pressing the button before the fixed time duration has passed interrupts the data acquisition 24 82 SUNACom User Manual Running SUNACom Fixed Time Acquisition The fixed time acquisition duration is 30 sec Periodic SUNACom opens a dialog showing the current SUNA clock time and the time of the next scheduled acquisition event After confirmation SUNACom passes control to SUNA which will remain in a low power state until the time of the scheduled data acquisition That data burst and any generated at a later scheduled time will be received by SUNACom Press the Stop button on the SUNACom dashboard to return to setup mode Periodic Acquisition fi The instrument s current clock time is 14 Oct 2011 12 15 28 UTC The nex periodic acquisition start time is 14 Oct 2011 12 16 05 UTC Polled SDI 12 APF SUNACom opens a dialog alerting you that SUNACom cannot acquire data for the configured operating mode After confirmation SUNACom returns to setup mode
41. em select SUNACom in the Programs section of the Start menu On a Mac OS X system select 4 Connect SUNA with the RS 232 Programming Cable or USB Programming Cable to the matching connector on your computer 5 If using the RS 232 cable connect the power leads to a 8 15 VDC power supply If connecting via USB the DC power supply is only needed for data acquisition When a USB connection is established and SUNA supports internal data logging the SUNA file system will appear as a USB MSC on the computer 6 On the SUNACom dashboard press the Connect button to establish a communication between SUNACom and SUNA As soon as SUNACom communicates with SUNA the other SUNACom functions are made active If the communication cannot be established see Troubleshooting for help 7 Press the SUNA Settings button to view or change the current SUNA settings Press Cancel to use the existing settings or press Ok to upload modified settings 8 SUNA is now ready for data acquisition 6 82 SUNACom User Manual Quick Start Data Acquisition Test Do a data acquisition test to evaluate SUNA performance and if necessary reset the calibration baseline 1 Setup SUNA as described in the preceding section If communicating via USB cable connect the power leads to a 8 15 VDC power supply 2 Run the SUNA Self Test from the Advanced submenu in the Sensor menu to confirm all systems are performing according to specification If an err
42. es must be downloaded from a SUNA before they can be replayed Displaying data in SUNACom works without conversion into a format suitable for plotting by another application Such a conversion can be done for ASCII data formats by loading the comma separated value csv file into a spreadsheet program Binary data conversion requires additional steps one option is use SUNACom to convert binary data into an ASCII format another is to use a custom data conversion program The Replay Logged Data feature is accessed via the SUNACom View menu A dialog will open requesting the user to specify e the package file e the raw data file e the calibration file optional The package and calibration files are located in the default document folder on the computer or alternatively on the SUNACom installation CD The default document folder is operating system dependent Windows XP C Documents and Settings SUSERNAME My Documents Satlantic SUNA Windows Vista Windows 7 C Users SUSERNAME My Documents Satlantic SUNA Mac OS X Users Home Satlantic SUNA The data file locations either when logging in SUNACom or when down loading data from SUNA are freely selectable by the user The Default Data Directory is used initially and can be located via Preferences in the SUNACom menu After all replay items are specified press the Finish button to view the data The interface is identical to the one used in the Data Acquisition
43. ference between the reference spectra in two calibration files Nitrate Reprocessing SUNA on board nitrate processing is governed by a set of processing settings and the currently active calibration file SUNACom nitrate reprocessing uses the SUNA spectrum data and generates nitrate concentrations based on alternate processing settings Reasons to reprocess nitrate concentrations fall into three broad categories 1 The SUNA settings were selected incorrectly and reprocessing can correct for this An example would be a SUNA deployed in a seawater environment but configured for fresh water processing 2 Over an extended deployment the SUNA output may have drifted and consequentially the calibration file was updated The data are then reprocessed using the updated calibration file and the drift between the original and reprocessed nitrate concentrations can be evaluated 3 The SUNA deployment was in an seawater setting and correlated water temperature and salinity measurements were collected The temperature and salinity values can be combined with the SUNA spectral data to obtain more accurate nitrate concentrations Sakamoto et al 2009 Reprocessing is accessed via the SUNACom Data menu The nitrate reprocessing dashboard located in the SUNACom Dashboard area presents input output and reprocessing options in a single interface 54 82 SUNACom User Manual Running SUNACom Reprocessing Dashboard T x Nitrate P
44. g oO amp 30 000 25 000 a 20 000 15 000 10 000 5 000 o 2 000 a i c 1 500 oO oO oO T 1 000 a T w 500 a 0 200 225 250 275 300 325 350 375 400 Wavelength nm y 0 10 2 30 40 E 50 60 The spactra graph Spectra Graph Configuration The Spectra Graph can be configured by pressing its Configure button The Configure Graph dialog is displayed to allow the option to have its graph history to be either unbounded or to be limited to a specified number of graphs When the graph history is limited to a specified number the slider will only allow this number of the most recent Spectra Graphs to be viewed amp Configure Graph E Graph History Unbounded Graph History Limit 1 29 82 SUNACom User Manual Running SUNACom The spactra configuration dialog Zooming on the Spectra Graph Zooming in and out of the Spectra Graph can be accomplished in several ways The first is by the use of the zoom buttons at the top left of the Spectra Graph The Zoom In and Zoom Out buttons will zoom the plots around the date centre 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 cha
45. g SUNACom 8 82 SUNACom User Manual Installing SUNACom System Requirements Microsoft Windows e Operating system Windows XP Vista 7 8 e Processor 2 6 GHz Intel Pentium IV or equivalent e Memory 2 GB e Disk space 1 GB of free disk space Apple Mac e Operating system OS X 10 7 Lion or OS X 10 8 Mountain Lion e Processor Dual Core Intel e Memory 2 GB e Disk space 850 MB of free disk space 9 82 SUNACom User Manual Installing SUNACom Installation Find the SUNACom software installer on the included CD ROM or under the Download tab at http www satlantic com If upgrading over a previously installed version of SUNACom close any SUNACom application currently running and uninstall SUNACom before proceeding with the new installation Make sure that no SUNA is connected via USB to the computer when installing SUNACom Run the SUNACom installer Agree to the license terms and confirm the default installation location The final step includes the option to install the USB Serial Driver Check this option if your SUNA supports USB communication Otherwise SUNACom will not be able to communicate with SUNA via USB 10 82 SUNACom User Manual SUNACom Overview SUNACom Overview SUNAConm is a graphical user interface designed to support SUNA setup and operation SUNACom version 3 works with SUNA sensors running firmware version 2 Among the SUNACom capabilities are e SUNA configuration e
46. g deployment including cable and receiver After connecting SUNA to an analog data logger or measureing device select the DAC Calibration entry in the Advanced sub menu in the SUNACom Sensor menu The dialog that opens gives DAC output control to the operator Pressing the Lowor High button will create an analog signal corresponding to the lower or upper value that is set for the Nitrate DAC Range see Advanced Settings More details on how to derive and apply the calibration coefficients are provided in the Analog Output section of the user manual DAC Calibration SES High Close Help The DAC calibration dialog SUNA Firmware Upgrade All SUNA operation is controlled by the firmware a program loaded on the sensor Satlantic may occasionally release firmware updates for SUNA and SUNACom provides an interface to upgrade to a new firmware Caution SUNA cannot operate without a valid firmware When upgrading the firmware the existing firmware is erased and the new firmware is written to memory If the write process is interrupted for example by a loss of power SUNA may enter a non responsive state In case of a problem contact Satlantic for support The following steps are required to upgrade to a new firmware 1 Open the Firmware Upload Dialog via the Advanced selection in SUNACom s Sensor menu 2 Enter the location of Satlantic s Firmware Upgrade File 52 82 SUNACom User Manual Run
47. he default baud rate will be preselected in the SUNACom connect dialog The default com port will be preselected in the SUNACom connect dialog SUNACom will attempt to wakeup a SUNA that could be asleep for maximum wakeup attempts when a serial port is selected for connecting to a SUNA SUNACom will wait for the duration of the response timeout for a response from SUNA The timeout is used when initially connecting and for most SUNA commands SUNACom will wait for the duration of the file listing timeout for a response from SUNA to a listing of files command When automatic serial connection is checked SUNACom will automatically connect at program start up using the default values The default data directory specifies where data files will be written If the prompt at startup box is checked SUNACom asks for the default data location at SUNACom startup Display Preferences 7 d Preferences x x A j General Display Message Logging Nitrate Units pM Y Use UTC Time Performance Optimization Settings V Enable Real Time Display J Enable Data Acquisition Monitor 7 Enable Spectra Graph 7 Enable Time Series Graph 7 Enable Total Absorbance Graph Ge Lip SUNACom display preferences panel 19 82 SUNACom User Manual Running SUNACom SUNACom can present nitrate concentrations in the SUNA native nitrate unit of UM or it can convert those to mg l SUNACom can write t
48. html SUNA communicates over serial port at 8 data bits no parity 1 stop bit and no flow control SUNA is initially set to 57600 baud but that rate can be changed to 9600 19200 38400 or 115200 Upon powered SUNA writes an initial output message before either acquiring data or entering low power sleep for polled or scheduled operation The initial output message should appear at the terminal emulator If non readable text occurs the terminal emulator baud rate is incorrect and needs to be 72 82 SUNACom User Manual Troubleshooting changed When connected at the correct baud rate sending the character possibly a few times will cause SUNA to enter its command line indicated by the SUNA gt prompt If a connection cannot be established please contact Satlantic support Using a USB Cable 73 82 SUNACom User Manual Troubleshooting Connected With Problem If the USB to Serial connection is working in a terminal emulator but not in SUNACom there may be a permission problem with the installer In SUNACom open the application log file under the view for stack traces and look for the error message AP Event Details Date Tue Feb 15 13 00 10 AST 2011 Mode DisconnectedMode Event Code TAM 6811 Action SerialConnectAction Message i i i Gre B If this message occurs it is due to a permission problem with serial communication on Mac OS X with RXTX the library SUNACom uses for serial communication
49. ibution to the absorbance AF 9 12 Absorbance RMSe The square root of the mean of the sum of the squared differences between the reprocessed measured and the fitted absorbance This value provides a measure for the quality of the fit Absorbance at 254 nm AF 9 12 The reprocessed absorbance at 254 nm Absorbance at 350 nm AF 9 12 The reprocessed absorbance at 350 nm The reprocessed absorbance Data Frame Frame Header The Satlantic SAT SUNA reprocessed absorbance NABS frame header and the 4 digit serial number as SATNABSnnnn e g SATNABS1234 The date from the input data frame as YYYY MM DD e g 2012 11 10 The date from the input data frame as hh mmiss sss e g 09 08 07 654 Reprocessed nitrate en The nitrate concentration reprocessed using the specified settings Channel 1 bl The absorbance for the first spectrometer channel at wavelength 1 Channel N AF 3 12 The absorbance for the last spectrometer channel at wavelength N 59 82 SUNACom User Manual Running SUNACom Replay Logged Data The replay logged data feature plots the content of SUNA data log files Three plots are generated Atime series of selected data A spectrum plot for each measurement An absorbance plot for each measurement optional The data files were collected either while data were acquired in SUNACom or logged internally while a SUNA was operating autonomously In the latter case the data fil
50. ified by the sample interval For instance an interval of 6 hours will trigger data acquisitions at 00 00 hr 06 00 hr 12 00 hr and 18 00 hr This acquisition sequence will be repeated indefinitely The offset measured in seconds shifts the start time of the data acquistions An offset of 300 seconds 5 minutes will change the start times in the above example to 00 05 hr 06 05 hr 12 05 hr and 18 05 hr Within these intervals the acquisition duration is given by either the number of light frames if sample based or the duration in seconds if time based If the duration of an acquisition event is longer than the time between acquisition events the next event will be missed r SUNA Settings General Telemetry Advanced g Operational Mode Periodic Periodic Mode Settings Sample Interval 1 hr X Offset 0 sec Frame based operation Time based operation Light Frames 5 frames Sample Averaging SUNA supports internal averaging when acquiring data When averaging multiple spectra are measured and averaged The nitrate concentration based on an average spectrum is more precise than the concentration based on a single spectrum When averaging the SUNA frame rate is reduced Deployment Characteristics 36 82 SUNACom User Manual Running SUNACom The estimated frame rate of the instrument is derived from the Spectrometer Integration Period the Number of Samples in Average the Baud Rate and
51. ile During data acquisition SUNACom expects to receive data frames and writes these if requested to a data log file Unexpected data are SUNA generated messages or data frames that were corrupted during transfer and are thus not recognized by SUNACom The Location of the message log files is determined by the computer operating system and printed at the bottom of the dialog 21 82 SUNACom User Manual Running SUNACom Sensor Menu The Sensor menu interaction SUNA Frequently used Sensor menu functions are also accessible via buttons on the SUNACom dashboard Only the Connect function is available when a connection between SUNACom and SUNA has not been established As soon as SUNACom communicates with SUNA the other functions become accessible The following functions are provided Connect establishes communication between SUNACom and SUNA When connected the label changes to Disconnect selection of which terminates the communication Start begins a SUNA data acquisition When acquiring data the label is changed to Stop selection of which ends the data acquisition SUNA Settings determine how SUNA operates during a data acquisition Transfer Files provides an interface to offload SUNA data log files to the computer and to manage the SUNA file system Update Calibration resets the SUNA measurement baseline Set Clock synchronizes the SUNA internal battery backed clock to the computer clock Summary Report writes th
52. imes in the SUNA native UTC time or it can convert those times to the computer local time zone During data acquisition results can be displayed in real time the data acquisition can be monitored and graphs of the spectra and the absorbance and a time series of the data can be displayed The respective check boxes determine the default display when starting a data acquisition Besides providing a consistent display layout reducing the number of displays can improve SUNACom performance SUNACom Log Files SUNACom generates message log files that track the SUNACom execution and the data exchange between SUNACom and SUNA Messages are logged in human readable text format These log files are useful for tracing SUNA configuration and use over time They can also aid in diagnosis and troubleshooting both by the operator and by Satlantic support Messages are logged automatically unless the default configurations are changed Access to the message logging configuration panel is via the SUNACom menu a i Preferences Ex 7 A lt 3 Ly General Display Message Logging Message Logging Logging Level INFO 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 File Location C Users glenn AppData Roaming Satlantic SUNACom 3 0 eventlogs 20 82 SUNACom User Manual Running SUN
53. ing Troubleshooting Unexpected behaviour can originate in all system components e The SUNA hardware e The SUNA cable e The USB or serial input port on the computer e Computer software setup or configuration Such problems show themselves in the following ways 1 SUNACom cannot connect to SUNA 2 SUNACom connects and reports problems 3 SUNACom connects without reporting problem but the SUNA performance is unexpected Many issues can be resolved by following the steps outlined below However if the problems persist please contact Satlantic support at http Avww satlantic com support 70 82 SUNACom User Manual Troubleshooting Cannot Connect to SUNA Please consult the hardware troubleshooting section regarding cable pin outs on how to test for proper functioning of the cables and on monitoring power consumption After making sure that the SUNA has been properly set up please perform the verification steps appropriate for the cable and port that are used e Using a Serial Cable with a USB to Serial Converter e Using a Serial Cable with a Serial Port e Using a USB Cable Using a Serial Cable with a USB to Serial Converter See instructions supplied with your specific USB to Serial adapter for instructions Mac OS X does not come with USB to Serial port adapter drivers The following DigiKey USB to Serial converters are known to work with SUNA e UC232R 10 e US232R 10 They require a FTDI USB Serial
54. is created when data acquisition starts for the first time after power has been cycled and e By File Size a new file is created whenever the current data log file reaches the specified maximum size r SUNA Settings General Telemetry Advanced Data Transmission Serial Baud Rate 57600 X Transmitted Frame Format FULL_ASCII Data Logging Instrument Logging Frame Format FULL_ASCII Log File Creation Method Maximum Size 2 MB Lun Canet eta a 38 82 SUNACom User Manual Running SUNACom SUNA Advanced Settings The advanced settings panel collects SUNA settings that rarely require modification They all have the potential to change the SUNA performance and should be changed with caution In unusual environmental conditions high turbidity consistently high nitrate conditions unusual water contaminants changes to the advanced settings can improve the SUNA performance However under normal conditions changes to these settings typically degrade the data quality The impact of changes to these settings is not easily observed and some effects may only occur during a deployment but not in a test or laboratory setting Thus please consult with support personnel at Satlantic when unsure about the impact of a change The advances settings are part of the settings dialog which is opened from either the SUNACom communication dashboard the tool bar or via
55. l SUNACom Overview SUNACom Dashboard Connection Mode Suns Connection Status Connected Available Lamp Time 977 hours 98 Available Disk Space 1 854 MB 99 SUNA Clock Time 20 Dec 2012 20 07 04 UTC SUNA Serial Number 167 FW Rev 2 2 8 TE SUNA Settings ma Transfer Files oe Update Calibration start The SUNACom dashboard Connection States and Operation Mode Disconnect Disconnect The SUNACom connection states Disconnected When SUNA is disconnected data reprocessing becomes available Transition from Disconnected to Connected SUNACom shows the mode as transition while exchanging commands with SUNA Connecting can take many seconds because some operating modes leave SUNA in a power conserving state or because some activity has to be interrupted before commands can be exchanged If the connection cannot be established the mode changes back to disconnected Disconnecting SUNA from the computer while keeping it powered leaves SUNA in its last mode either at setup or in data acquisition Because it is disconnected you can no longer monitor SUNA activity Connected at Setup 14 82 SUNACom User Manual SUNACom Overview At the setup state SUNACom gives access to administrative functions like SUNA settings file management and calibration update It is also possible to start a data acquisition or to disconnect from SUNA
56. n occur on MAC OS X when the user account has no administrator proviledge Data Acquisition Data acquisition and in particular nitrate measurement is the main function of SUNA When power is applied SUNA executes the configured operating mode and initiates data collection and output When SUNACom connects to SUNA it interrupts the data acquisition and opens the SUNA command interface At the command interface SUNA setup and maintenance functions are available The operator can manually start and later stop data acquisition via the Start button on the dashboard or the respective entry in the Sensor menu In this way SUNACom can serve as a controller and data logger for SUNA Even when deploying independently of SUNACon a test data acquisition is useful to confirm that the selected configuration executes as expected During a data acquisition SUNACom displays and optionally logs the transmitted data The operating mode determines SUNACom s execution sequence after the data acquisition is started SUNACom can run a data acquisition only for SUNA s autonomous operating modes Continuous fixed time and periodic The other operating modes polled SDI 12 APF require a controller to trigger data collection Configuration and simulation of custom controllers is outside the scope of SUNACom Continuous SUNACom exits setup mode and hands control to SUNA SUNA then autonomously and continuously acquires data The data stream will be rec
57. new reference spectrum 44 82 SUNACom User Manual Running SUNACom a 4 Calibration Wizard Es Steps Acquiring spectra data from SUNA wizard 2 of 4 1 Fillthe sampling volume with DIW Status 2 Acquiring spectra data x from SUNA Processing 3 Compare new reference Processing Progress spectrum to current Sa 27 4 Upload calibration file with new reference spectrum lt Back Next gt Finish Cancel Help Reference Update Dialog Acquire reference spectrum Step 3 Compare the new reference spectrum to the previous one SUNACom plots the relative difference of the new reference spectrum versus the reference spectrum in the currenlty active calbration file Under most conditions the relative change will be relatively flat and below 5 for wavelength above 250 nm and can be more sloped below 250 nm Large changes below 210 nm are possible but of no concern with respect to nitrate measurements If the relative change is not a smooth curve but shows erratic changes conditions were not stable The update should then be cancelled at this point and restarted If erratic changes persist please contact support at Satlantic 45 82 SUNACom User Manual Running SUNACom rc i 2 3 amp Calibration Wizard Steps Fill the sampling volume with DIW Acquiring spectra data from SUNA Compare new reference spectrum to current Upload calibration file with new
58. nges the zoom behaviour Zooming still occurs along the Wavelength Axis for all plots but along the Range Axis for the clicked on plot only Click on the Spectra 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 Absorbance Graph The total absorbance graph displays calculated absorbance from 210 nm to 370 nm The total absorbance display was added to SUNACom as an alternative to the Spectra Graph to help users interpret and understand sample spectra Interpreting the absorbance graph requires no prior knowledge of the typical shape of the measured spectra When measuring a DIW sample the absorbance graph should be flat As absorbing species such as nitrate and bromide are added to samples the absorbance will increase exponentially with decreasing wavelength 30 82 SUNACom User Manual Running SUNACom FE Output Spectra Graph 2 Time Series Graph 8 Absorbance Graph Processed Nitrate Data Viewer 2 alak B a Total Absorbance 0 100 0 075 4 0 050
59. ning SUNACom 3 Press the Upload button to start the upgrade 4 SUNA recognizes invalid firmware files and rejects those 5 The complete firmware upgrade takes no longer than 2 minutes 6 After the upgrade has been completed SUNA is disconnected from SUNACom the user must manually re establish the connection Upload Firmware File SUNA Firmware File Browse The Upload Firmware dialog Upload Instrument XML File SUNACom uses the Instrument XML file which is kept on the SUNA to interpret SUNA data frames Without a valid Instrument XML file SUNACom will not be able to display replay or reprocess SUNA data The Instrument XML file upload permits fixing a corrupted XML file Please use this function only when advised by Satlantic The upload function is accessed via the Upload Instrument XML Flle entry in the Advanced sub menu in the SUNACom Sensor menu 53 82 SUNACom User Manual Running SUNACom Data Menu The data menu functions are used to either reprocess replay or convert previously collected SUNA data These operations do not require connection to a SUNA e Reprocess data using different calibration files or processing settings e Replay Logged Data displays graphs of previously acquired SUNA data in SUNACom e Convert Raw Data writes frame sensor values to an ASCII file e Convert APF Data generates full ASCII frame from the APF frames e Compare Calibrations plots the relative dif
60. ns like spreadsheet programs APF frames require special applications for data analysis SUNACom offers the binary to Full_ASCII frame conversion to facilitate analysis of data that were acquired in APF format Furthermore APF data frames have to be converted before SUNACom reprocessing is possible The Convert APF Data function is accessed via the SUNACom Data menu A dialog will open requesting the following input The instrument package file specifies the output Full_ ASCII frame format The instrument package file can be found in the Calibration files folder SUNACom install disk or in the default application folder on your computer Windows XP C Documents and Settings SUSERNAME S My Documents Satlantic SUNA Windows Vista Windows 7 C Users USERNAME My Documents Satlantic SUNA Mac OS X Users Home Satlantic SUNA The raw data files contain the APF frames that are to be converted e The output directory will contain the SUNACom generated output files one for each selected raw file The names of those files are based on the raw file name The original file extension is removed the file name is augmented by the _APF string and the new extension will be csv 64 82 SUNACom User Manual Running SUNACom 4 Convert APF Data Files to Full ASCII xm Standard Instrument Package File Instrument Package File Browse F temp SUN amp _0165_001 xml Raw Data Files Browse F temp 4000
61. nvenient method of keeping track of SUNA configurations over time A configuration record is useful when evaluating data acquired during a deployment When reprocessing such data the reprocessing configuration especially the calibration file should match deployment configuration However if it turns out that the deployment configuration was not optimal the report is a starting point for alternate configurations In order to generate a summary report connect SUNACom to a SUNA Then open the Summary Report dialog via the Sensor menu Summary Report x Operator Name SUNA Summary Report Comments File Name Report 21 12 2012 0923 pdf v View Report Directory C Users SUMA Documents Browse Save Report Cancel Help The summary report includes the name of the person generating the report and an optional comment The report file will be written to the specified location using the selected name Command Terminal The command terminal provides a direct connection to the SUNA command line whenever SUNACom is in setup mode SUNACom uses the subset of the SUNA commands required for the operating modes it supports Unsupported operating modes polled APF and SDI 12 can be configured and tested via the 48 82 SUNACom User Manual Running SUNACom command terminal All SUNA commands are listed in the hardware section of the manual The SUNA output will be shown in the Setup Console window availabl
62. 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 Mac OS X it is the Alt key Spectra Graph The Spectra Graph pane shows the raw counts for both the light and dark frames The display is located in the upper right part of the application window in a tabbed pane The counts in the spectrum are proportional to the amount of light reaching the sensor The dark counts result from thermal noise and the light intensity is proportional to the light counts minus the dark counts The light spectrum is the result of the SUNA lamp output and the spectrometer sensitivity The spectrometer operates in the 190 390 nm range The in air or in DIW spectrum is always flat below 28 82 SUNACom User Manual Running SUNACom 200 nm and then has four or five peaks The peaks are some 25 nm apart in the lower and up to 50 nm apart in the upper wavelength range Spectra Graph Ewe Q Zoom In Q Zoom Out Auto Range V Wavelength Axis V Range Axis Configure Spectra 60 000 55 000 50 000 46 000 oa 2 40 000 Lu 35 000
63. of the year The extension is based on the frame type logged to the file e BIN Binary frames e CSV ASCII frames with comma separated values The file manager supports transfer of data files from SUNA to the computer and deletion of the files on SUNA and on the computer Files that are transferred are not automatically deleted from the SUNA file system Log files Internal logging of messages if supported by the SUNA is controlled via SUNA Telemetry Settings Log files contain output diagnostics generated by SUNA during its operation These messages can be used to verify that a deployment executed as planned and can aid in troubleshooting problems that may have occurred The file manager supports transfer of log files from SUNA to the computer and deletion of the files on SUNA and on the computer Files that are transferred are not automatically deleted from the SUNA file system Reference Update Instrument Drift Over time SUNA sensors will exhibit drift which is due to changes in the optical components Drift can be separated into two types External and internal change External change is due to deposits on the SUNA 42 82 SUNACom User Manual Running SUNACom windows and can be eliminated by carefully cleaning the windows with cotton swabs and isopropyl alcohol Internal change cannot be eliminated instead the SUNA baseline is reset by a reference update Reality Check The SUNA is prepared for a reality
64. on files may reside in SUNA memory but only one file is active at a given time indicated by a green background in the file manager The user can select an alternate active calibration file in the file manager via the Set Active button The file manager supports transfer of calibration files from the computer to SUNA and deletion of the files on SUNA and on the computer A file that is uploaded automatically becomes the active calibration file 41 82 SUNACom User Manual Running SUNACom Over time the reference spectrum can drift and affect SUNA accuracy SUNACom supports the generation of calibration files containing an updated reference spectrum Please consult the SUNA Reference Update manual section for details on SUNA drift Data files Internal logging of data if supported by the SUNA is controlled via SUNA Telemetry Settings When configured files are automatically generated during data acquisition All file names begin with a single letter A C or D followed by a seven digit number and have either a BIN or CSV extension The first letter of the file name is determined by the logging type A Start a file with an incremented number whenever SUNA is powered up e C Log continuously and start a file with an incremented number after a selected file size has been reached e D Log all data collected over a calendar day into a single file The file number is composed of the four digit year and the three digit day
65. onents 0 5 0 4 v 0 3 oO S 02 fe B01 lt oO 1 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 2 2 Wavelength nm BaseLine Salinity amp Temp Salinity Nitrate Nitrate Time Series 61 5 3 4 1921 1922 19 23 19 24 1925 19 28 19 27 1928 19 20 19 30 19 31 1932 1933 19 34 1035 1936 1937 19 38 19 39 19 40 19 41 Time Original Nitrate Reprocessed Nitrate 0 100 200 A time line example for reprocessed data The reprocessed nitrate data frame Frame Header AS 11 The Satlantic SAT SUNA reprocessed nitrate NPRO frame header and the 4 digit serial number as SATNPROnnnn e g SATNPRO1234 Date AS 10 The date from the input data frame as YYYY MM DD e g 2012 11 10 Time AS 8 12 The date from the input data frame as hh mm ss sss e g 09 08 07 654 Original nitrate UM AF 4 9 The nitrate concentration from the input data frame Reprocessed nitrate we The nitrate concentration reprocessed using the uM specified settings SWA seawater 12 The seawater concentration reprocessed using the specified settings 58 82 SUNACom User Manual Running SUNACom T SWA AF 9 12 The temperature seawater concentration reprocessed using the specified settings The Oth baseline contribution to the absorbance There will be N Baseline Order 1 baseline contributions AF 9 12 The Nth baseline contr
66. oor at approximately 2 5 absorbance units The absorbance threshold offers a method of controlling the accuracy of the processed data by removing low quality parts of the fitting range from processing However in waters with high broad band absorbance a low threshold can lead to an exclusion of all wavelength in the fitting range In this case increasing the threshold leads to successful processing albeit at the expense of reduced data precision e A seawater calibration s deployed in fresh water option should be checked if the deployment was in fresh water The accuracy and precision of the nitrate concentrations will be significantly higher On the other hand processing data acquired in seawater with the deployed in fresh water option checked will result in nitrate concentrations that are incorrect Temperature salinity correction is available if the calibration was done for seawater Temperature salinity correction requires that the SUNA data are accompanied by water temperature and salinity measurements TS data The TS data can be obtained from SUNA frames if data were acquired in APF operating mode and a controller was sending the data for on board processing and incorporation into the data stream 56 82 SUNACom User Manual Running SUNACom e Alternatively TS data can be obtained from an external file The data in that file must be in the following ASCII format YYYY MM DD hh mm ss Temperature C Salinity PSU 2012
67. or is reported see Troubleshooting for help 3 Place DIW into the SUNA sampling volume to check for instrument drift 4 Press the Start button on the SUNACom dashboard to start a data acquisition SUNACom will display graphic plots of SUNA sensor data as they are received in real time SUNA instruments are typically run either periodically for short bursts of 1 30 seconds or continuously for a duration of many minutes or longer Time the test such that it matches the planned use and deployment Ideally immerse SUNA in water with a temperature similar to the temperature at the deployment location The reason to timing the test is that internal warm up causes a slight drift in the measured nitrate concentration Matching the timing to that of the deployment scenario improves the accuracy of the comparison For continuous data acquisitions the internal temperature typically stabilizes after 8 10 minutes 5 If the nitrate concentration is between 2 uM or above 2 uM the nitrate concentration is within specification and SUNA is ready for deployment 6 If the nitrate concentration is below 2 uM or above 2 uM the instrument has drifted Stop the data acquisition then press the Update Calibration button to reset the SUNA measurement baseline 7 After the update repeat the data acquisition test to make sure that the measured nitrate concentration is within specification 7 82 SUNACom User Manual Installing SUNACom Installin
68. pectrometer light measurement reporting average standard deviation and minimum to maximum range The minimum count of the light spectrum should be within 5 standard deviations of the dark spectrum average and the maximum count of the light spectrum should not exceed 55000 counts Test result Either ok test passed or Error 1 test failed DAC Calibration The DAC digital to analog converter is an optional SUNA feature It generates an analog signal representing the measured nitrate concentration as a voltage and as a current The Electrical Specification section of the user manual details the electrical pin out and the voltage and current ranges If the analog output feature is not present on SUNA the DAC calibration will not be available in SUNACom 51 82 SUNACom User Manual Running SUNACom A DAC Calibration is necessary for converting the analog signal into nitrate concentrations This conversion inverts the operations performed by the SUNA in conjunction with the receiver which are measure the nitrate concentration SUNA generate the corresponding analog signal SUNA DAC converter e transmit the signal cable measure the signal receiver ADC converter The transformations in this sequence are linear thus both the generation and the inversion of the analog signal can be expressed by a linear equation The best calibration results are achieved by using a setup that is identical to the one used durin
69. ration time adjustment turned off Concentration frames and data recorded via SDI 12 do not contain spectral data and thus do not permit reprocessing 55 82 SUNACom User Manual Running SUNACom Processing Settings Enable Raw Data Checksum Validation Fitting Range 216 5 gt 240 0 nm Max Absorbance Threshold 1 3 Seawater Calibration Deployed in Fresh Water The nitrate processing settings panel Processing settings are initially set to default values and hidden from view For situations outlined below changing these settings can improve the data quality The enable raw data checksum validation option should be checked to prevent using corrupt raw data frames from being processed Sometimes it may be required to disable this option to allow raw data frames to be processed when it is known that the checksum values have been modified after the raw data was acquired The fitting range defines the wavelength interval to be used for processing The default range of 216 5 240 nm contains the absorption interval for nitrate and seawater At shorter wavelength seawater typically causes complete extinction causing a poor signal to noise ratio At higher wavelength non characterized substances may absorb biasing the processed concentrations The absorbance threshold controls the quality of the processed data The accuracy of the measured absorbance starts to decline at 1 3 absorbance units and approaches the noise fl
70. rocessing Settings Instrument Package Calibration File Nitrate Data Files C Users SUNA data SUNA165 40000010 csv C Users SUNA data SUNA_0165_001 xml Browse C Users SUNA data SUNA165D CAL Browse X Processing Settings Browse ly ly Output Data Files Output Directory Temperature amp Salinity Correction C tmpSUNA Browse Single Output File Z Graph Results L Process Selected File s The nitrate processing dashboard The following input files are required for data reprocessing The instrument package file xml format describing the SUNA data The calibration file for the reference spectrum and the extinction coefficients of the chemical species Proper management of calibration files is crucial for obtaining high quality data Over time SUNA drift requires updates to calibration files Thus the calibration file used for processing must match the time of the data acquisition The series of calibration files unless manually deleted is kept in SUNA internal memory The data files to be reprocessed are first loaded into the dashboard Then all or a subset of those files are selected for processing Nitrate processing requires spectral data which are recorded in full ASCII full and reduced binary and APF frames Reduced binary and APF frames allow reprocessing for seawater deployments APF frames only allow reprocessing of data that were collected with the integ
71. ropriate calibration file For SUNA with internal data logging file transfer is needed to retrieve data that have been logged during a deployment SUNACom opens its file manager via the Transfer Files button that is located on the dashboard Three tabs in the file manager list SUNA files according to their type data log and calibration files An alternative log file and data file management mechanism is available when SUNA is connected via USB Then SUNA also operates as a USB Mass Storage Device offering a operating system dependent interface and higher data transfer rates c File Manager a Data Files Log Files Calibration Files Local Filesystem Instrument Filesystem C Users SUNA Documents Browse Name Date Size SNAO167A CAL 2012 12 21 13 17 34 9984 Name bas Sie SNA0167B CAL 2012 12 21 13 17 40 10240 SNAQL678 CAL SNA0167B CAL 2012 12 21 13 16 18 10162 Select All Delete Select All Delete Set Active Close Help The file manager Calibration Files A calibration file contains data required to convert a spectral measurement into a nitrate concentration The calibration data are the wavelengths of the spectrum the extinction coefficients of chemical species and a reference spectrum relative to which the measurement is interpreted Additionally a calibration file contains auxiliary information detailing its origin and the interpretation of its contents Multiple calibrati
72. s 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 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 SUNA 2008 03 80 10 25 21 UTC SUNACom ISC 6804 ERR Calculate file identity failed java io FileNotFoundException C Program Files Satlantic SUNACom 1 0 0 CURRENT CAL The system cannot fin at java io FileInputStream open Native Method 75 82 SUNACom User Manual Troubleshooting at at at at at java io FileInputStream lt init gt FileInputStream java 106 com satlantic isus sunacom Ancillary calculateIdentity Ancillary java 205 com satlantic isus sunacom ui actions simple SerialConnectAction attachedToPort SerialConnectAc com satlantic isus sunacom ancillary AttemptConnectPort run AttemptConne
73. s have been cleaned This second reality check measures the internal drift and its result determines if a reference update is required Data from both reality checks should be logged and kept for future reference If there is a significant difference between the initial and the second reality check more frequent window cleaning is necessary Alternatives to more frequent services are wipers or pumped systems Reference Update Using SUNACom Step 1 Fill the sampling volume with DIW Clean the windows with a cotton swab and isopropyl alcohol Then place DIW into the sampling volume Make sure there are no air bubbles sticking to the windows 43 82 SUNACom User Manual Running SUNACom a Calibration Wizard Steps 1 Fill the sampling volume with DIW 2 Acquiring spectra data From SUNA 3 Compare new reference spectrum to current 4 Upload calibration File with new reference spectrum Fill the sampling volume with DIW wizard 1 of 4 The Active Calibration File on the SUNA is SNAO167M CAL Clean the windows with a cotton swab and isopropyl alcohol Then place DIW into the sampling volume Make sure there are no air bubbles sticking to the windows Acquisition Mode Operational Mode Continuous lt Back Finish Reference Update Dialog DIW sample Step 2 Acquire the new reference spectrum SUNACom automatically acquires a number of reference spectra which are averaged for the
74. tate From there you can start a data acquisition Stopping the data acquisition brings SUNACom back to the setup state The functions of the dashboard are also available through the Sensor menu and via the tool bar Dashboard Layout The dashboard contains three sections e The top of the dashboard shows the connection status e The central section provides information about SUNA The bottom section gives operational access to SUNA Information Connection Status SUNACom is either connected to or disconnected from a SUNA Available Lamp Time The nominal remaining life time of the lamp in hours Available Disk Space The space that remains in SUNA internal memory for data logging e SUNA Clock Time The time of the SUNA clock in the time zone specified in the Use UTC Time option in the SUNACom preferences Serial Number Tne SUNA serial number e FW Rev The firmware revision running on the SUNA Operation Connect Disconnect Establish communication between SUNACom and SUNA When connected the label changes to Disconnect selection of which terminates the communication SUNA Settings View and modify SUNA settings Update Calibration Update the reference spectrum in the calibration file Transfer Files Manage files in SUNA internal memory Start Begin a SUNA data acquisition When acquiring data the label is changed to Stop selection of which ends the data acquisition 13 82 SUNACom User Manua
75. the SUNA 1 Connect SUNA to the computer using the USB or RS 232 cable 2 In the SUNACom Dashboard press the Connect button 3 The SUNACom Connect dialog will open When using RS 232 select the SUNA baud rate It is usually 57600 If the baud rate is unknown check the Try All Baud Rates box When using USB the baud rate is ignored 4 Select the serial port the SUNA is connected to 5 Press the Connect button in the dialog 6 It may take up to 30 seconds to establish the connection and longer when Try all baud rates is checked z i Connect exa Baud Rate 5761 Try All Baud Rates connect Cancel Help The SUNACom connection dialog Failure to Connect A serial connection can fail for a number of reasons 1 The baud rate did not match Connect with the Try All Baud Rates box checked 23 82 SUNACom User Manual Running SUNACom 2 The serial port did not match Connect to the correct serial port If a connection cannot be established for any serial port baud rate combination please refer to the troubleshooting section of the manual A USB connection can fail for a number of reasons 1 The USB to Serial Driver was not installed This fail conditions is diagnosed when the SUNA mass storage device is visible to the computer but there is no serial port associated with the USB connection 2 The USB port is visible but cannot be accessed This problem ca
76. ults are output in the transmitted frame format A frame contains all or a subset of the values that were measured at that time Possible frame formats are Full ASCII contains all information in comma separated fields variable size typically 1600 1800 bytes 37 82 SUNACom User Manual Running SUNACom Concentration ASCII contains time stamp nitrate concentration absorbances at 254 and 300 nm and RMSE as a measure of the data quality Full Binary contains all information 632 bytes fixed size Reduced Binary contains part of the spectrum and some auxiliary sensors 144 bytes fixed size e APF contains the selectable part of the spectrum and some auxiliary sensors in comma separated fields Size is variable typically 300 400 bytes Reprocessing of data will not be possible for Concentration ASCII frames The frame type can also be set to None to switch off data output This is advantageous when logging data only internally because it increases the data acquisition rate Data Logging optional feature The instrument logging frame format is the frame format written to data log file during data acquisition The possible formats are the same as used for the transmitted frame format Selecting None turns internal data logging off The log file creation method determines when the SUNA creates a new data log file The options are e Daily a new file is created each midnight e By Power Cycle a new file
77. ying output from SUNA or during data handling The Window menu for control of the windows within SUNACom The Help menu for access to help items the user manual and Satlantic contact information 17 82 SUNACom User Manual Running SUNACom SUNACom Menu The SUNACom menu accesses functions that affect the running of the SUNACom application without impact on the connected sensor The following functions are available e Preferences determine the behaviour of the application when connecting to SUNA specify how SUNA data are displayed and fine tuning of the application log file generation e Exit closes the SUNACom application SUNACom Preferences SUNACom preferences determine the behaviour of the application when connecting to SUNA specify how SUNA data are displayed and fine tuning of the application log file generation These preferences persist from one SUNACom session to the next ensuring a consistent work flow The Preferences Dialog is accessed from Preferences in the SUNACom menu General Preferences r T Display Message Logging SUNA Connection Settings Default Baud Rate Default Com Port Maximum Wakeup Attempts Response Timeout File Listing Timeout F Automatic Serial Connection Default Data Directory C Users glenn Documents J Prompt at startup SUNACom general preferences panel 18 82 SUNACom User Manual Running SUNACom T

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