HydroSoft User`s Manual
Contents
1. HydroSoft 2 8 Software for HOBI Labs Optical Oceanographic Instruments User s Manual Revision G Hydro Optics Biology amp Instrumentation Laboratories DAM Lighting the Way in Aquatic Science www hobilabs com support hobilabs com Revisions G May 24 2010 Minor changes reflecting to HydroSoft update from 2 7 to 2 8 especially addition of Abyss transmissometer F February 19 2010 Formatting E June 6 2007 Corrected the formula for sigma correction in section 7 4 D October 22 2004 Many changes to support version 2 7 Major changes add Processing menu 10 3 Compare Calibrations command 10 3 4 change handling of Sigma calculation 7 4 changes to main data windows 4 1 command line processing 9 2 full formatting control of Spectral Plot windows 6 6 C June 27 2002 Many changes to support version 2 5 Major changes spectral plot windows section 6 6 calibration functions section 10 2 11 and separate Backscattering Calibration Manual support for multiple instrument connections section 4 1 6 B February 20 2002 Update address A February 22 2001 Current version 2 02 Update formatting Remove Draft designation add references in section 7 4 3 October 30 2000 describes version 2 01 TABLE OF CONTENTS 1 INTRODUCTION sasssa rss a sta in 1 ll SYSTEM REQUIREMENTS anode a e ee EHE EE GO EO C PEE PE2. Graph Previous Zoom section 6 3 2 Graph Auto Scale section 6 3 2 Instrument Connect section 5 1 Instrument Open Terminal section 4 3 start instrument Start Stop section 10 2 6 4 1 6 Multiple Data Windows If you open a data file while a data file is already open in the current window the file will be opened in a new data window You can also open a new empty window with the New Window command on the File menu Unlike in previous versions of HydroSoft all data windows are functionally identical and each window can support its own connection to an instrument Each new data window the currently selected calibration file as its default for displaying raw data However you can subsequently select a different calibration file or even a different instrument type in a particular window without affecting other open windows For more about calibration files see section 7 New data windows also adopt the graph settings of the current window 4 2 Spectral Plot Windows When viewing data from a HydroScat you can select Plot Vs Wavelength from the Graph menu to open a window that shows the spectrum of data at specific points or ranges of points in the data shown in a main window s graph For details see section 6 6 4 3 Terminal Windows Each data window has a corresponding terminal window that allows communicating directly to a connected instrument and viewing in raw form the same da
3. Each data window to which an instrument is connected can have its own terminal window See section 4 3 for details 10 24 Disconnect Severs communication with a connected instrument and closes the computer s COM port Before disconnecting offers the opportunity to put the instrument to sleep 10 2 5 Reset You should only need to use Reset in the unusual case of an instrument that will not wake up or communicate normally After asking you to confirm the command it sends a signal intended to reboot the controller in a connected instrument Specifically it asserts a continuous logical high on the RS232 transmit line for a period you specify The default period is 90 seconds which is sufficient to reset most HOBI Labs instruments Note however that the COM ports of some computers especially laptops do not produce enough voltage to activate this function on some a Beta and c Beta instruments If the reset command fails you may need to apply a voltage directly to the instrument s connector After a reset you may need to use the Connect command to re establish communications at the instrument s default baud rate and you may also need to allow the instrument some time to initialize itself before it will respond to connection attempts The longest time about two minutes is required by a c Beta or a Beta with full memory In most cases the required time will be much shorter 10 2 6 Start Stop The name of this command changes d
4. a data window attempt operation that requires a connection if a connection has not yet been established 5 1 2 Manual Connection If you click the Connect button HydroSoft will open the currently selected port at the selected baud rate Normally you need not select an instrument type because HydroSoft will always request identification information from the instrument If it receives a reply sufficient to identify the instrument it will proceed with the connection and close the dialog box If not it will notify you and ask whether to open the connection anyway In you instruct it to it will proceed on the assumption that an instrument of the type you designate is connected 11 5 1 3 Search Connection If you click Search HydroSoft will ignore the selected port and baud rate and attempt a connection to each port at each baud rate from 4800 to 57600 until it receives valid identifying information from an instrument The dialog box will automatically close if a valid connection is found 5 1 4 Load Calibration From Instrument Option If Load Calibration From Instrument is checked at the time an instrument is connected HydroSoft will prompt the instrument to transmit the calibration information stored in the instrument s memory This will override the currently selected calibration file if any section 5 4 for more information about calibration files 5 1 5 Open Port with Identifying Instrument If this option
5. Parameters Opens a dialog box in which you can set the parameters used to calculate the backscattering coefficient For details see section 7 3 10 3 7 Sigma Correction Parameters Opens a dialog box in which you can set the parameters used to adjust backscattering measurements to compensate for attenuation in the water See section 7 4 for complete details 10 4 Graph Menu 10 4 1 Plot Vs Depth Sets the graph in the current window to display data as a depth profile That is the measured parameters will be displayed with reference to the horizontal axis and the vertical axis will indicate depth 10 4 2 Plot Vs Time Sets the graph in the current window to display a time series That is the measured parameters will be displayed with reference to the vertical axis and the horizontal axis will indicate time 45 10 4 3 Plot Vs Wavelength Opens a spectral plot window as described in section 6 6 10 4 4 Zoom In Adjusts the axes of the graph in the current window to expand the center portion of the graph by a factor of 2 10 4 5 Zoom Adjusts the axes of the graph in the current window to double the displayed data range reducing the apparent extent of the data by a factor of 2 10 4 6 Previous Zoom Sets the axes of the graph in the current window to the settings they had before the last command that adjusted the zoom 10 4 7 Auto Scale Sets the axes of the graph in the current window to encompass the e
6. axis limit control whether the scale will be adjusted to the range of the data Note that the effect of auto scaling is intentionally limited in two ways 1 Auto scaling can only expand the axis ranges not contract them 2 Auto scaling only applies at the time new data are added to a graph either from a connected instrument or upon opening a file That is you can set 19 the axis limits to values that would exclude some existing data points regardless of whether auto scaling is on But auto scaling will expand the limits if new data that exceed the current limits are subsequently added These characteristics are especially useful when collecting data in real time from an instrument In real data it is not unusual for an outlying point to skew the auto scaling If this happens while you are collecting data you can re adjust the axis settings to exclude the outlying point but leave auto scaling on so that it will still accommodate new data 3 Graph Properties Scattering Auto Min 0 Max 0012 Time Auto Min 0 160 Save As Defaults Recall Defaults 6 3 2 Other Scaling and Zooming Options While you can enter exact numeric limits for each axis via the Graph Properties dialog box HydroSoft provides several more rapid options The Zoom In and Zoom Out commands and their toolbar equivalents contract or expand the axis limits by a factor of 2 The Auto Scale command and bu
7. from values presented Morel Optical Properties of Pure Water and Pure Sea Water Optical Aspects of Oceanography M G Jerlov and E S Nielsen eds Academic Press New York 1974 chap 1 pp 1 24 However by selecting the custom option you modify the model You can also remove the pure water factor entirely by choosing custom and setting the parameters to zero 7 4 Sigma Corrections Sigma correction is an adjustment to improve the accuracy of backscattering measurements in highly attenuating water Some light that would otherwise be detected as backscattering 15 lost to attenuation in the water between the instrument and the detection volume causing backscattering to be underestimated We compensate for this applying the following correction where is the uncorrected backscattering Sigma corrected b is calculated by using the sigma corrected f in the equation described in section 7 3 o K is a complicated function of the sensor s optical geometry but can be closely approximated by o K k exP kexp Kop Versions of HydroSoft prior to 2 5 used a third order polynomial approximation for sigma and the current version still uses this if the constant kexp is not present in an instrument s calibration data 27 where is the coefficient of attenuation for light traveling from the sensor to the sensing volume and back k is characteristic of the specifi
8. is checked when you connect HydroSoft will simply open the serial port at the baud rate you specify without communicating with the instrument in any way This allows you to use HydroSoft as a dumb terminal for troubleshooting or for communicating with devices HydroSoft cannot identify 5 1 6 Connection Options at Program Start The Preferences command under the File menu provides three options that select whether and how a connection is established when HydroSoft first starts Do Not Connect HydroSoft makes no connection at startup Restore Previous Connection H ydroSoft will open the Connect dialog and attempt to connect using the port and baud rate of the last successful connection Search For Instruments H ydroSoft will open the Connect dialog and click the Auto Search button For applications in which you regularly connect using the same port and baud rate the Restore Previous Connection option is usually the most convenient 5 1 7 Connecting to a Sleeping Instrument In some cases HydroSoft may not detect the presence of an instrument that is in its low power sleep mode If you have difficulty connecting to a sleeping instrument we recommend you use the instrument s magnetic switch to wake it before connecting 12 5 2 Collecting Real Time Data To start collecting data from a connected instrument click start lo select Start from the Instrument menu If no graph is visible when you start collection H
9. may also choose to apply the same K estimation technique that is applied to HydroScat instruments Prior to HydroSoft 2 7 was reckoned including the contribution of pure water Thus it and differed considerably at different wavelengths and the value of k appropriate to each channel was included in the calibration file Starting with version 2 7 Kp is defined to include only attenuation above and beyond that of pure water Values of k calculated with the former method are still included in calibration files for compatibility with previous versions but are not used by version 2 7 28 7 4 3 HydroScats Since HydroScats do not make a direct measurements of attenuation their K is estimated from a 0 4b where a is estimated from a priori data and b is estimated from the measured is calculated from the following model 4 a A 0 06 2 9 11 0 2 2 440 a 400 exp y 4 400 where the first term accounts for the contribution of chlorophyll and other factors that correlate with chlorophyll and the second term accounts for detrital material 2 is a function determined empirically by Prieur and Sathyendranath optical classification of coastal and oceanic waters based on the specific spectral absorption curves of phytoplankton pigments dissolved organic matter and other particulate materials Limnol Oceangr 26 4 671 689 and modified by Morel Light marine
10. necessary for the user to save it again before closing The number of data points graphs in HydroSoft can hold is limited to avoid excessive use of system memory The Maximum samples in a graph setting controls this limit Normally it can be set quite high but if HydroSoft strains the memory capacity of your computer you may choose to reduce it Note that the limit on points in a graph does not limit the number of data lines saved in files The only limit on how large data files may grow is available space on the disk on which they are saved Finally the Preferences dialog provides space to enter comments that will be saved in the header of every data file you create For example you may wish all files associated with a particular deployment to include the same identifying information 10 1 7 Print Graph Prints the current window s graph after presenting the following dialog box HS020733 2004 10 11 time3 raw HydroSoft Printer Wtweetyl exmark Orientation Added Information Portrait IV Title Landscape Graph to demonstrate printing Keep aspect ratio Legend Date Time Instrument Identification Marne of Data File Cancel Name of Calibration File 41 10 1 8 Export Graph Saves an image of the current graph into a graphics file in one of the following formats bitmap bmp Windows metafile wmf Enhanced metafile emf JPEG jpg JPEG format is not particularly well
11. plots see section 6 4 1 2 Mouse Pointer Coordinates Whenever the mouse pointer is within the plot area of a data window a small window that shows the data coordinates of the pointer appears in the upper left corner This allows you to determine the exact value of a particular data point simply by pointing at it This display reflects whatever units are shown on the graph axes If the plot contains two Y axes as for an a Beta or c Beta both Y values will be shown 4 1 3 Channels Panel The Channels Panel on the right side of the data window lists the parameters displayed in the current graph Normally these are the parameters of the current instrument but they may be different if you open a stored data file with different parameters If the panel is not visible click on the _ Show Channels E bb510 button to open it Click to hide this panel Channel name Click to select color Click to hide or show this channel Latest value 0 00653 E bb 20 You can choose which channels 0 00511 are displayed in the graph by clicking the dp check boxes to the left of each channel name You can also change the color vm 5 sama N sigma corrected or used to display each channel by clicking RS T uncorrected values on the colored box to the right of the aiidas are plotted both are always saved to files check box Note however that colors you select this way only apply to the currently displayed graph To change t
12. through the Graph Properties dialog box To open it select Properties from the Graph menu or double click on a graph When you open the dialog box it contains the settings of the current graph or if no graph is open the default settings 6 2 Default Properties Default properties are those applied to newly created graphs or applied when you use the Apply Default Properties command in the Graph menu In addition to their unique controls each of the three tabs in the Graph Properties dialog box contains buttons labeled Save as Defaults and Recall Defaults When you click Save as Defaults all the properties in the currently active tab are stored as default properties for subsequently opened graphs Clicking Recall Defaults will replace the current properties in the dialog box with the defaults but they will not be applied unless you click the OK or Apply button 6 3 AXIS Scales 6 3 1 Dialog Box Settings The Scales tab in the Graph Properties dialog box controls the limits of each axis in a graph It contains properties for Time Depth Scattering and Attenuation or Absorption axes although these do not normally all appear in one graph If the properties apply to a particular graph only the controls appropriate to that graph will be enabled If you open the Graph Properties dialog when no graph is open all controls will be enabled for purposes of setting the defaults and the Apply button will be disabled The Auto options for each
13. type new size into Marker Size text box If you set the size to 0 zero markers will appear 21 change the width of lines between points type new number into the Line Width text box If you enter 0 zero no lines will appear Note that if you set both Marker Size and Line Width to zero your data will be invisible 6 5 Graph amp Grid Settings 3 Graph Properties Graph amp Grid Data Markers Scales Grid On Colors Grid Style Graph Graph Grid Interior Exterior Solid Dashed Dotted Save 5 Defauits Recall Defaults OK Apply Close The Graph amp Grid tab in the Graph Properties dialog box controls the color and style of the grid the color of the graph interior the part containing the data and the color of the graph exterior the border area containing the axis labels 6 6 Spectral Plots If data from a HydroScat are shown in a main data window you can select Plot Vs Wavelength from the Graph menu to open a window that shows the spectrum of data at specific points or ranges of points in the data shown in the main window s graph Initially a single trace shows the spectrum measured at a particular depth or time The slider control at the bottom of the window selects the point on the parent graph whose spectrum is shown and you can drag the slider to view the changes in spectrum throughout the data series You can view an average of data
14. 00 17 516 CHANGING B AUD RATE nie teet te ee tor 18 5 7 SPECIAL MESSAGES FROM INSTRUMENTS 0 00202 00000 01000000000000000000 nete rena annee 18 6 PLOTTING DATA ss 19 6 1 GRAPH PROPERTIES 2 0200000000000000000000000000000000 eset tetra nn nes eerte 19 6 2 DEFAULT PROPERTIES enhn nnne nennen 19 E 19 OA eec etie e teo ert De eere iore eee eroe 21 6 5 GRAPH amp GRID 5 5 1 0 000000000 00000000000000000000000 22 6 6 SPECTRAL PEOTS cre Sevens pee tete sat UY 22 6 7 PRINTING AND EXPORTING 8 1 00000 000000 enne ennt tete nnn sees eene tensa sess stern ases eene 24 7 CALIBRATION DATA 50554 sana 25 GEOADINGAALDIBRATIONS cid iter rrt t sab rh ta ne Dt Ur eese d s 25 12 VIEWING AND EDITING CALIBRATION 25 7 3 BACKSCATTERING COEFFICIENT CALCULATION 2 00000000000000000000000000 26 SIGMA CORRECTIONS re IB Een nen e e s 27 8 DATA LB cr 31 Sl gt ZRAWODATA a ee tente ettet ra esas a 31 8 2 CALIBRATED DATA s
15. 00 2 INSTALLATION You must be logged as a user with administrator privileges order for HydroSoft to install all the necessary files on Windows XP or later systems If not the installation program will present an error message and you must log on using a different account with the necessary privileges HydroSoft versions 2 5 and later install some files differently from previous versions If you have an earlier version installed on your machine we recommend uninstalling it before installing version 2 5 or later 2 1 Basic Installation HydroSoft is delivered as self installing executable either on a CD ROM or as a download from http www hobilabs com It has the name InstallHydroSoftXXX exe where is the version number e g 280 This program operates similarly to most other Windows installers 1 Run the installer program 2 Decide whether you would like the HydroSoft application stored in the default directory shown If not select a different directory 3 Click Next to start the installation 4 When the installation is complete click Finish to exit 2 2 Installation Notes You need not reboot your computer after installation unless the installer program specifically instructs you to do so A HydroSoft item will be added to your start menu and the directory you selected during installation will contain HydroSoft exe the HydroSoft program astar csv and aw csv files us
16. 22 over a range of points by holding down the shift key while dragging the slider from left to right HS020733 2004 10 11 time3 raw HydroSoft t o o o o cu 5 a m Double click anywhere plot area to open Properties dialog 00 440 460 480 500 520 540 560 580 600 620 640 660 Wavelength nm Selection Clean Water Add Scattering Med Scattering Depth 0 1 to 0 1 Capture Drag to select a spectrum Click to save the Click to clear Shift drag to average a range current selection captured traces As in the Main Data window you can double click any portion of the plot to open a Properties dialog box in which you can adjust many aspects of the display You can also zoom in on a portion of the data by click dragging in the plot area and zoom out to include the entire data set by selecting Auto Scale from the Graph menu The Copy Scale From Parent command adjusts the vertical scale to match that of the main data window from which the spectrum window was launched Clicking the Capture button freezes the currently displayed spectrum but leaves the slider active so that you can compare the captured spectrum to others You can capture many spectra for simultaneous display Each time you capture a spectrum a dialog box prompts you for descriptive text to identify it in the legend 3 Legend Text Text to identify the captured t
17. Basic Sampling Sample Rate 100 per second Sample Period 1 00 seconds Start Delay 2 seconds Sleep when memory fills Start on power up Burst Mode Burst made on Burst length 100 seconds Burst interval 30 minutes Burst Warmup seconds Total Duration hours Burst length 0 seconds Burst interval 60 minutes Make these settings nonvolatile Reload Close HydroScat Sampling Options Reload Close a Beta c Beta Sampling Options When the Sampling Options dialog is first open it may take several seconds for the current settings to be retrieved from the instrument Similarly when you click the Apply button there will be a noticeable delay while HydroSoft transmits then confirms the new settings This confirmation is important because it allows you to check that the settings were entered as you intended Instruments may reject settings they cannot support for example burst lengths that are longer than the burst interval 5 3 1 General Options You should consult your instrument s documentation for details that may not be covered in this overview of sampling options Sample Rate and Sample Period by definition have an inverse relationship Changes you make to one will automatically affect the other Also note that the period is actually the controlling parameter and has a resolution of 0 01 seconds Therefore some exact sample rates are not available For examp
18. Click Download Depending the quantity of data and baud rate downloading may take some time Status messages and a graphical indicator will show the download progress clear instrument s memory after verifying the desired casts were downloaded click Delete All Click Close to dismiss the dialog box 5 4 2 Details Depending on the type of instrument and the number of casts stored loading the directory may take a number of seconds status message in the upper left corner indicates if the directory is loaded as above or if it is in the process of loading 16 memory status line indicates how much of the instrument s memory is presently used You can select arbitrary groups of casts for downloading select a contiguous group of casts click on the first item in the group then shift click on the last item or hold down the shift key while using the arrow keys To select or unselect non contiguous casts control click on them or hold down the control key while using the arrow keys to move through the directory and press the space bar to select or unselect casts Data are always collected in raw form If the Create calibrated data dat files option is checked a calibrated file will also be created for each downloaded cast The calibration currently in effect for the main data window will be applied to these data see section 7 for more information about calibrations Because of the way Hydro
19. RLES TES 1 12 INSTRUMENT FIRMWARE 68 1 2 TINS TAB EA TION eis 3 27 5 5 saa nr karin 3 2205 INSTALLATION NOTES a 3 2 3 UREMOVING HY RO S ET te cesta season 4 QUICK START uoce 5 Als WINDOWS cic 5 usa d na SE EE 7 41 MAN WINDOW 7 42 SPECTRAL PLOT WINDOWS ccccesssssccececeesesseceeececeeesessaecescecesenesececeeeceesesaeaeceeecensaseaeceeeesenenseaeees 10 43 TERMINAL WINDOWS E aet tec e e XU EE e e AER HA 10 5 COMMUNICATING WITH INSTRUMENTS eee eese eese eee sanns 11 Sil CONNECTING is eee E eere ot eve terere PE ec edle vede ec dece tree redd 11 8 2 2 e ss 13 5 375 25205 td uee e eed aee rep eee cedes tite 13 5 4 CRETRIEVING LOGGED DATA centeno defer e ee ER LUI a 15 5 5 SETTING INSTRUMENT DATE AND TIME 0 21 2 2 2022002000000000000000000000000
20. Scat and x Beta instruments handle their memory it is not possible to delete individual casts you can only erase the instrument s entire memory Abyss transmissometers however do permit deleting individual casts 5 5 Setting Instrument Date and Time To set the real time clock in a connected instrument select Set Date Time from the Instrument menu The following dialog box will appear Set Instrument Time amp Date Instrument Time Time to Set 10 18 2004 10 18 2004 Set to Computer 12 47 23 10 59 50 AM Set Manually Set Time By default the instrument clock will be set to match your computer s clock when you click the Set Time button However you can also select the Set Manually option enter an arbitrary date and time in the appropriate fields and set the instrument to that date and time When it sets the time HydroSoft also requests the instrument to echo the new time so that you can confirm it has been set properly This can take several seconds 17 5 6 Changing Baud Rate The Change Baud Rate command on the Instrument menu opens a dialog box in which you can select a new baud rate for communication between the connected instrument and your computer If you select a new baud rate and click OK HydroSoft sends a command at the current baud rate to the instrument instructing it to change rates HydroSoft then changes the baud rate of your computer to the new rate It the instrument does not respon
21. a connected instrument and have not yet been saved you will be prompted to do so 10 1 6 General Preferences Opens the following dialog box HydroSoft Preferences Connect when program starts Do not connect C Restore previous connection C Search for instruments Automatically recall last selected calibration file Request user to name files when they are created Maximum samples in a graph 50000 Does affect graphs that open now Header to include in all data files i Pinafore The Connect when program starts options control whether HydroSoft will automatically attempt to connect to an instrument when it starts up For a complete description see 5 1 6 HydroSoft keeps a record of the calibration file you most recently selected If Automatically recall last selected calibration file is checked HydroSoft will load this 40 each time you restart the program If not calibration will be loaded until you explicitly select it For more about loading calibrations see 7 1 If Request user to name files when they are created is checked HydroSoft will present the Save As dialog box whenever you create a file with the New command In some deployment circumstances it is preferable to name a file and designate its location when it is first opened rather than when it is closed as is more conventional Once a file is named HydroSoft continuously saves its data so that it is not
22. c instrument and is included in its calibration file 018 set so as to satisfy the requirement that o K 21 where K is the attenuation excluding that of pure water of the water in which the instrument was calibrated That is k exp amp K When exp the calibration is performed with well filtered water is near zero and is for practical purposes 1 at all wavelengths When processing raw data HydroSoft selects the method for estimating K based on the instrument type and also allows adjustment of various parameters used for the different instruments Unless they thoroughly understand the optical considerations involved users should leave these set to their default values Calibrated data files also include uncorrected backscattering values so that users can apply their own corrections outside HydroSoft if they prefer If a and b or c measurements are available at the appropriate wavelength s users can calculate accurate sigma corrections using the relationship Kp a 0 4b where all values exclude the contribution of pure water 7 4 1 The value measured by a Beta is equivalent to Therefore it can be used directly in the sigma calculation This gives the most accurate correction possible and no user variable parameters are needed 7 4 2 c Beta For c Beta measurements HydroSoft estimates that K pc where p is set to 0 6 by default but can be changed by the user Users
23. d after a baud rate change it may be that a communication error interfered with the transition In this case try changing back to the previous rate or use the Search option in the Connect dialog box to find the correct rate 5 7 Special Messages From Instruments In some circumstances an instrument may generate an important message marked in the data stream by an exclamation point that HydroSoft is not expecting If it receives such a message HydroSoft will present it to you in this manner Message from Instrument H2000326 Can not change time during a cast In this example a user has attempted to set the time of a HydroScat 2 s clock while the instrument was logging which the instrument does not permit H2000326 at the beginning of the message is the serial number of the instrument that sent it for identification in case you have multiple instruments connected HydroSoft will beep and bring this window to the front whenever such a message is received If multiple messages are received they will accumulate in the window until you close it or click the Clear button If HydroSoft s terminal window is open these messages will be displayed there instead of the special Message window 18 6 PLOTTING DATA Data plots in HydroSoft may show data read from an existing file or received in real time from a connected instrument 6 1 Graph Properties Dialog Box graphical characteristics of a data plot are controlled
24. ed by the sigma correction algorithm HydroSoft not required for all instruments and aw csv is no longer required but is included for backward compatibility a Help Files folder including HTML and related files and Unins000 exe and Unins000 dat a program and supporting data for uninstalling HydroSoft 2 3 Removing HydroSoft 1 2 4 From the Start menu select Settings then Control Panel Double click on the Add Remove Programs icon Select HydroSoft from the list of programs Click the Add remove button OR Open the directory into which you installed HydroSoft Double click on the unins000 exe icon which runs the un installer For HydroSoft versions before 2 10 the uninstaller was named unwise exe 8 9 3 QUICK START If necessary install HydroSoft as described in section 2 Connect an instrument to a serial port on your computer Select HydroSoft from the Windows Start Menu Click select Show Terminal from the Instrument menu Click or select Connect from the Instrument Menu details in section 5 1 Click the Search button After a short time HydroSoft should identify the instrument load its calibration and close the Connect dialog box In the main data window select Plot Vs Time from the Graph menu Click start or select Start from the Instrument menu 10 If no data are visible after a short time click El and the pl
25. epending on whether the connected instrument is currently sending data Start instructs the instrument to begin sending data in accordance with its own sampling schedule see 5 3 and Stop instructs it to cease If no instrument is connected when you select Start HydroSoft will open the Connect dialog box section 5 1 1 10 2 7 Sleep Wake The name of this command changes depending on the current state of the instrument Sleep puts the connected instrument into its low power sleep state 43 from which it must be woken with the Wake command before further communication is possible unless you Connect to the instrument which also wakes it 10 2 8 Sampling Options Opens a dialog box that allows you to set the parameters governing the sampling schedule of the connected instruments See section 5 3 for details 10 2 9 Set Date Time Opens a dialog box that allows setting the date and time of a connected instrument s real time clock See section 5 5 for details 10 2 10 Get Data From Instrument Opens a dialog box that displays a directory of casts stored in the connected instrument s memory and allows downloading data into computer files See section 5 4 for details 10 2 11 Calibrate Opens a window with controls for collecting and processing backscattering calibration data Details are contained in a separate Backscattering Calibration Manual available from HOBI Labs 10 2 12 About Instrument Opens a window showing the t
26. ficient b which must be calculated from Aw and a priori knowledge about the relation ship between X y and b for typical particles HydroSoft calibrated data dat files always include the calculated b values and normally also include However to maintain compatibility with older software that did not accommodate you can turn off the Include beta in dat files option in the Backscattering Parameters dialog box shown below b is calculated from b 2ny B B 5 where 2 is the scattering of pure water in the range of angles measured by the sensor and b is the backscattering coefficient of pure water 7 is the coefficient of proportionality between f and for particles and while it is not constant for all particle types it does not vary much in typical natural waters For most applications the default values for either salt or fresh water will provide the most accurate results but users with detailed knowledge of the issues may wish to change the parameters using the Backscattering Parameters command from the Processing menu which opens the following dialog box 26 Backscattering Parameters Backscattering coefficient calculation Pure water scattering calculation b 227 B B by B CD aZ C Morel Salt Water C Morel Fresh Water C Custom X C Use values from calibration file Use this value 1 08 By Ag 15 5 52 508 04 0 ss Pure water scattering values calculated
27. he default colors used to display data in new graphs you must use the Graph Properties dialog section 6 1 Select whether The Channels panel may also include controls to select display options For backscattering sensors a pair of radio buttons enables you to select whether Sigma correction is applied to the current data see section 7 3 for more about sigma correction 4 1 4 Status Display A text field at the top of the data window indicates whether an instrument is connected and if so whether it is currently sampling stopped or sleeping Various other messages may appear in the status field when appropriate If an instrument is connected four more fields appear at the bottom of the window These show time elapsed since the first point in the current graph was received depth of the instrument voltage of the sensor s batteries external supply internal temperature of the sensor Note that the status parameters are only updated when an instrument is actively transmitting data If the instrument has been stopped or sleeping for some time the values may be invalid 4 1 5 Toolbar buttons Toolbar buttons in the data window provide shortcuts to commands that also appear in the menus as listed below E File Save As section 10 1 4 1 File Open section 10 1 2 S File Print Graph section 10 1 7 a Graph Zoom In section 6 3 2 IS Graph Zoom Out section 6 3 2
28. he full path and name of a single data file to process and calfile is the full path and name of the calibration file to apply Note that the file names are separated from each other by a semicolon HydroSoft will process the given file according to the most recent settings in the Backscattering Parameters and Sigma Parameters dialogs then exit If successful it will create a dat file with the same name and in the same directory as the source data file 37 10 MENU COMMAND REFERENCE 10 1 File Menu 10 1 1 New New causes the currently open data file if any to be closed and a new empty file to be created Because new HydroSoft data originate only from instruments new files can be created only when an instrument is connected to the data window If you select this command when no instrument is connected it will first present the Connection dialog box also see 5 1 1 If you have selected the Request user to name files when the are created option in the Preferences dialog box see 10 1 6 you will be prompted to enter a name and location for the new file and to specify whether a calibrated data file will be saved If not or if you click the Save Later button in the File Name dialog box the data will be saved in an untitled file and you will be prompted for this information at the time the file is closed 10 1 2 New Window Opens a new empty data window section 4 1 10 1 3 Open Allows you to display an existing raw or cal
29. ibrated data file It presents a dialog box with familiar controls for selecting the drive and directory in which to browse and the type of files to list Although HydroSoft by convention saves raw and calibrated files with the and dat extensions respectively it does not require these extensions in order to read files correctly In order to open a raw data file HydroSoft requires that an appropriate calibration file be loaded If the currently loaded calibration does not match the data in the file you select HydroSoft will offer the opportunity to select a different calibration or to cancel the operation 10 1 4 Save As Opens a dialog box through which you specify the name and location for a file containing the currently displayed data If the current data are from a connected instrument both the current data and subsequently received data will be automatically saved into the file you specify If the data are from an existing file a new copy of the data will be created 39 Depending on the origin of the data you may have the option of saving either a raw file calibrated file or both Data from a raw file be saved as raw calibrated or both e Data from a calibrated file can only be saved as calibrated e Date from an instrument must be saved as raw but may also be saved as calibrated 10 1 5 Close Closes the currently displayed graph and corresponding file If the data in the graph are from
30. ime HydroSoft starts up If you have more than one data window open in HydroSoft you can select a different calibration file for each one The most recently selected file in any window will be saved as the default 7 2 Viewing and Editing Calibration Data You can see the details of the current calibration by selecting View Calibration from the Processing Menu This opens a dialog box whose format and behavior depend somewhat on the type of instrument to which the calibration 25 applies Refer to the documentation of each instrument for information about its calibration Normally you should not need to modify calibration data for an instrument and the fields in the Calibration dialog box are locked to discourage casual changes However you can unlock most fields by clicking on the lock icon in the dialog box Because correct calibration files are critical to the accuracy of your data use care when modifying them To reduce confusion we encourage you to enter a description in the comment field provided of any changes you make To save a copy of the currently loaded calibration select Save Calibration from the Processing menu 7 3 Backscattering Coefficient Calculation Backscattering sensors like HOBI s measure the value of the volume scattering function commonly represented as X v where w is the scattering angle within a fixed range of angles However many applications call for a closely related parameter the backscattering coef
31. ing bbParams are those described in section 7 3 31 The strings under the heading of Channels are the labels that appear in the Channels panel of HydroSoft data windows see section 4 1 2 The line marked as ColumnHeadings contains a comma separated list including identifiers for each parameter in the data lines 32 Header HydroSoftVersion 2 7 CreationDate 05 14 04 22 14 06 FileType dat DeviceType HydroScat 2 DataSource d HSoft Test FilesM4 5 00 raw CalSource d Instrument Calibration Files hs2 H2000324 000405 cal Serial H2000324 Config W1B3R1S012 SigmaParams ad400 01 aStarFile C Program Files HOBI Labs aStar csv awFile C Program Files HOBI Labs aw csv bbTildeValue 015 1 gammad 011 gammay 014 ExponentialFit False bbParams PureWaterModel Custom bb0 0 beta0 0 lambda0 525 gammaLambda 4 32 chi FromCalFile Channels bb470 bb676 1676 ColumnHeadings Time Depth bb470 bb676 1676 bb470uncorr bb676uncorr f1676uncorr Data 36622 0810034722 5 349999 2 200723 02 0173337 5 193215 04 0188008 0160407 5 193215E 04 Gl 1 Regardless of instrument type time and depth appear as the first two parameters in the data lines Times are stored as double precision real numbers corresponding to the number of days since midnight January 1 1900 This is the native format of dates and times in Microsoft Excel 8 3 Raw Decimal Data Raw decimal data may be needed for trouble
32. le if you enter a rate of 3 per second the actual value will be set to 3 03 which is the inverse of 0 33 the nearest available period In both examples above the burst mode parameters are inactive because burst mode is not on To edit the burst mode parameters you must first check the Burst Mode On option 14 Burst Interval is the time between the starts of successive bursts For example if Burst Length is set to 10 seconds and Burst Interval is set to 1 minute the sensor will sleep for 50 seconds between bursts 5 3 2 HydroScat specific Options HydroScat sensors have additional sampling parameters that do not apply to x Beta sensors Sleep when memory fills is self explanatory Start on power up is only relevant for instruments without batteries or whose batteries may be disabled whether or not intentionally Make these settings nonvolatile controls whether the settings will remain in effect even if the sensor is reset or loses power Total Duration controls whether burst mode casts will automatically halt after a specified time If it is blank or zero burst mode casts will continue indefinitely until halted by a user full memory or low battery HydroScat 6s have additional parameters for controlling their two fluorescence channels Because these channels share the receivers of two backscattering channels you can choose whether they are devoted to backscattering only to fluorescence only or time shared between the two func
33. ntire current data set 10 4 8 Apply Default Properties Sets all colors markers and axis settings in the current graph to their default values Default values are set through the Graph Properties dialog box See section 6 2 for details 10 4 9 Properties Opens the Graph Properties dialog box allowing adjustment of axis settings display colors and other aspects of graph appearance section 6 1 for complete details 10 5 Window Menu The Window menu lists currently open Data windows and also any Terminal Spectral Plot and Calibration windows associated with each Data window Selecting a window from this menu brings it to the front The menu also includes items for arranging multiple windows in a stack or tiling them side by side or one above the other 46
34. ot will zoom as needed to show all data 11 Double click on the graph or select Properties from the Graph menu to open the Graph Properties dialog box details in section 6 1 12 Adjust the display parameters according to your preferences 4 WINDOWS 4 1 Main Data Window Main data windows of which you may open several simultaneously contain controls for connecting to and controlling instruments as well as complete graphical display of live data or data retrieved from files Connect Instrument Terminal Button Status View Button Mouse Currect Calibration File Coordinates Zoom Buttons click to view gt 18020733 21104 10 11 time3 raw HydroSoft S rocessing Kraph Help e AARE JE E 93 5 minutes 0 0102 m 5 22 0 0102 93 5 minutes 0 0102 m B bb442 0 0104 bb676 a in M area un TY 0 00474 a mid bb488 lior 0 00832 bb555 0 00758 bb510 0 00653 620 0 00511 EM 555 0 0001 81676 0 0001 Sigma C Sigma Correct gt Ld 5 o o c E a E uu f e pue Time o 106 8 min 134 V 26 6 Elapsed Time Depth Supply Voltage Internal Temperature 4 1 1 Data Plot A data plot appears whenever a data file is open You can select whether the data are displayed as a function of depth or of time with commands on the Graph menu For full details on data
35. photosynthesis a spectral model with geochemical and climatological implications Prog Oceanogr 26 263 C is the chlorophyll concentration in mg m which can be set by the user as can Vy 90400 b is estimated b b b b where is the backscattering probability which can be set by the user The numerator of this expression is the uncorrected b excluding that of pure water The Sigma Correction Parameters dialog box is shown below with typical settings for a HydroScat sensor The default settings are appropriate for most cases The main exception is if chlorophyll levels are high and can be estimated it may be appropriate to adjust the value of C Prior to HydroSoft 2 7 the equation for absorption also included a term for pure water 29 2 Sigma Correction Parameters 0 015 C Program Files HydroSoft aStar csv p 30 8 DATAFILES For information about retrieving internally logged data from an instrument see section 5 4 Data may be stored raw form that 15 in the form they transmitted from an instrument or in calibrated form or both We strongly recommend you save your raw data files for two main reasons First under some circumstances you may wish to apply a revised calibration to existing data Second raw files contain some housekeeping information that can be useful for troubleshooting in the event of a problem Therefore when collecting data from an instrument H
36. race in the legend to 142 7 meters Cancel 23 By default this text is set to indicate the depth or range of depths the spectrum represents If the parent window shows data versus time rather than depth time values will be shown Clicking the Clear button removes all captured spectra from the plot If the parent window is receiving data from a connected instrument and the Live Update option is checked the spectrum display will update each time a new sample is received Live Update does not affect captured spectra The scale of the backscattering axis is the same as that of the graph in the parent window If you change the scale in the parent window while a spectrum window is open the spectrum window s scale will also change when you next bring it to the front 6 7 Printing and Exporting Graphs You can print the graph from a main data window by selecting Print Graph from the File menu For details see section 10 1 7 In a spectral plot window this command appears on the window s Graph menu You can also export a plot to a graphics file with the Export Graph command For details of exporting see section 10 1 8 24 7 CALIBRATION DATA In general data are received from instruments in raw form and must be converted to calibrated units The coefficients required for this conversion are unique to each instrument and may be revised from time to time when the instrument is recalibrated HydroSoft requires an approp
37. riate calibration to be loaded before it can plot or store calibrated data from an instrument or raw data file In addition to the instrument s calibration parameters the calibrated results from backscattering measurements depend on values controlled with File menu commands Backscattering Parameters section 7 3 and Sigma Correction Parameters section 7 4 7 1 Loading Calibrations Calibrations can be loaded either directly from a connected instrument or from a file on the host computer To load an instrument s calibration check the Load Calibration From Instrument option while connecting to the instrument see section 5 1 To load a calibration from a file choose Select Calibration File from the Processing menu If you select a new calibration file while an instrument is connected or while a raw data file is open HydroSoft will only load it if it is of a matching type HydroSoft will inform you if the type does not match It will also warn you if the serial number of the instrument does not match that contained in the calibration file but it will offer you the option of loading it even if the serial numbers do not match Once a calibration file is loaded it remains in effect until a different one is loaded When you exit HydroSoft it stores the name of the current calibration file If the Automatically recall last selected calibration file option is selected in the Preferences dialog box the file will be reloaded the next t
38. shift clicking and select or deselect individual files by Ctrl clicking Once you start processing all the selected files will be processed The processed files will use the same base names as the source files with their extensions set to They will be saved in the directory you specify If 36 you wish to save them the same directory as the raw files from which they generated you can avoid having to select that directory manually by checking the Same location as raw files option 9 1 2 Making Raw Decimal Files The process for making raw decimal files from hexadecimal files 15 identical to that described above except that there is no need for a calibration file Controls relating to the calibration file will thus be disabled Depending on the instrument you are using and its current configuration its files may not contain hexadecimal data If you select files without hexadecimal data they may appear to be converted but the resulting dec files will be empty However the original file are always preserved When you select the Make Raw Decimal Files option an additional Include Housekeeping checkbox will appear allowing you to control whether housekeeping data will be included in the file in addition to the primary optical data 9 2 Command Line Processing You can call HydroSoft from the Windows command line or from a batch file with the syntax HydroSoft datafile calfile where datafile is t
39. shooting or to review housekeeping data such as supply voltages and instrument temperature HydroSoft generates decimal data files from raw files but cannot read or graph them 33 9 PROCESSING RAW DATA FILES Processing in HydroSoft consists of applying the appropriate calibration data and user selectable parameters as described in section 7 This happens automatically whenever you view or download data from an instrument or open a raw data file for viewing However you can also process files in batches without displaying them in two ways 1 With the Process Raw Files command on the Processing menu 2 By calling HydroSoft from the Windows command line 9 1 The Process Raw Files Command The Process Raw Files command on the Processing menu allows rapid processing of multiple raw files converting them either to dat files containing fully calibrated data or dec files containing raw data in decimal rather than hexadecimal form These processes are controlled by the following dialog box 35 Process Raw Data Files Frocessing Make Calibrated Files C Make Raw Decimal Files Calibration File D Manufacturing Products HScats HS6 Individual Instruments HS33 IF Browse Raw Files to Process Directory containing source files al Instruments HS33 IRD2X2004 9 Service Cal Preservice Cal 2004 10 File name filter Eligible Files raw H5020733 2004 10 11 dKtime an4 1 A Select All H5020733 2004 10 11 dk
40. suited to line graphics but is offered since it is widely used and can produce a high degree of compression HydroSoft offers three levels of JPEG compression The most compact files have the lowest quality but are generally still quite legible 10 1 9 Close Window Closes the current data window and any accessory windows associated with 10 1 10 Exit Closes all HydroSoft windows first prompting you to save any unsaved data and quits the program 10 2 Instrument Menu When an instrument is connected to a data window the title of this menu changes to the instrument type for example HydroScat 6 The menu title is Instrument when no instrument or one of unknown type is connected 10 2 1 Connect Opens a dialog box in which you specify how to connect to an instrument through the computer s COM port See section 5 1 1 for details HydroSoft must go through the connection process before it can communicate with an instrument although it may be set to do this automatically when it starts up see section 10 1 6 10 2 2 Change Baud Rate Opens a window in which you can select a new baud rate for communication between the currently connected instrument and your computer Also see section 5 6 42 10 2 3 Show Terminal Opens a terminal window that displays the raw output from a connected instrument In the terminal window you can also type commands to the instrument and view its responses This is not required for routine operation
41. ta from instruments internal memory e providing an ASCII terminal interface for direct communication with instruments and collecting and processing data for calibrating backscattering sensors 1 1 System Requirements HydroSoft requires Windows 95 98 2000 NT 4 0 XP Vista or 7 HydroSoft and the files required to support it occupy a maximum of about 10M of hard disk space Communicating with instruments requires an RS232 port which may be implemented with a USB Serial adapter 1 2 Instrument Firmware Requirements Some HydroSoft functions require that instruments have a certain level of firmware internal operating software installed It is always possible to connect an instrument and communicate to it through the terminal window in the same manner as with a simple terminal program however some functions may not be available with some instrument firmware versions You can determine the firmware version of your instrument by connecting it through a terminal emulator program or through HydroSoft s terminal window and sending the VER command 1 2 1 a Beta and c Beta Firmware versions earlier than 1 39 do not support downloading of calibration data and the raw data will be in decimal format 1 2 2 HydroScats HydroScat instruments with firmware earlier than version 1 60 may not be identified correctly or provide downloading of data 1 2 3 Abyss 2 Not all sampling options are available in firmware version 1
42. ta that are displayed graphically in the main data window It contains the same Instrument menu status display and instrument control buttons as the main data window These controls produce the same results whether you use them in the terminal window or in the main data window Terminal windows contain Command Response and Data areas that display information sent to and from the instrument Characters you type while the Terminal window is active appear in the Command area and are simultaneously sent to the connected instrument Command responses and other informational transmissions from the instrument appear in the Response area Data transmissions appear in the Data area 10 5 COMMUNICATING WITH INSTRUMENTS 5 1 Connecting To communicate with an instrument you must connect it to a serial RS 232 communication port on your computer and HydroSoft must open the port at the correct baud rate Many operations also require that HydroSoft know what type of instrument is connected Therefore HydroSoft queries each instrument to identify itself at the time of connection 5 1 1 Connection Dialog Box Connect To Instrument Status Connection Com Port Baud Rate Instrument Type Com 2 57600 v unknown Load Calibration From Instrument Search Close Open port without identifying instrument This dialog box appears each time you select Connect from the Instrument menu click on the Connect button
43. te ar eda ch eO TRUE eT a A str ar 31 8 3 DECIMAL aa dec tees erre A EO RE ESO E E TEUER 33 9 PROCESSING RAW DATA FILES eee einn ineo ano eo e eerta ne Eae Po aaa ono Ro noo ree Vae Ro Sp ae kao ne eina 35 9 1 THE PROCESS RAW FILES 2 12 1 1 24244200000000000000000000000001010000000000 ass ener terns nennen 35 9 2 COMMAND LINE PROCESSING eese e enne nete nete nass ente 37 10 MENU COMMAND REFERENCE eoo en oso oae onto pn Ge eee on En pa oa s a sans eue ean ro ns las 39 101 OERLE MENU isss sasssa ee ce te de uc fee utt dere de cst aes ordeo tet 39 10 2 INSTRUMENT MENU 2525 ses ceres evi e oe err deii 42 10 33 52 cele 44 iii 10 4 GRAPH MENU 10 5 WINDOW MENU 22 a tr d eme erento tumet s iv 1 INTRODUCTION HydroSoft supports HOBI Labs HydroScat 6 HydroScat 4 HydroScat 2 a Beta c Beta and Abyss 2 instruments by e collecting live data received through RS232 port applying instrument specific calibrations to incoming data storing raw and calibrated data files plotting live and stored data as a function of depth or time controlling sampling rate and other instrument parameters retrieving logged da
44. time 4 2 _ H5020733 2004 10 11 dktime gn5 1 Show only files rnatching HS020733 2004 10 11 dktime gn5 2 Select None calibration file H5020733 2004 10 11 dktime gn5 2 H5020733 2004 10 11 dktime gn5 4 Use Shift click to select HS020733 2004 10 11 dk_1 raw groups of files HS020733 2004 10 11 dk_2 raw ei uere P H5020733 2004 10 11 dk 3 raw H5020733 2004 10 11 gn raw H5020733 2004 10 11 time raw Save Processed Data Files To C Documents and Settings Administratori My Documents Browse Same location as raw files Process Close 9 1 1 Making Calibrated Data Files When Make Calibrated Files is selected you need to specify a calibration file to be used You can type the path and name of the file directly or use the Browse button to open an Open File dialog box You must also select the file or files you wish to process using the familiar drive and directory list controls The list in the center right of the dialog box shows those files that are contained in the drive and directory you specify and whose names match the File name filter you specify If Show only files matching calibration file is checked as it is by default HydroSoft will check the contents of the files and list only those that contain data from the instrument type and serial number specified by the selected calibration file You can select a single file or an arbitrary group of files from the list Select a contiguous group of files by
45. tions See the HydroScat 6 User s Manual for more details 5 4 Retrieving Logged Data The Get Data From Instrument command enables you to view a list of casts stored in an instrument s memory transfer casts from the instrument to files on your computer and erase the instrument s memory Casts you transfer are stored in individual files whose location and base name you specify The cast number 15 appended to the name of each file 5 4 1 Basic Procedure Select Get Data From Instrument on the Instrument menu dialog box like the following will appear 15 HydroScat 2 Logged Data Loaded Memory Status 686439 1001471 bytes 68 free Load Directory Start time Duration Samples Delete All 1 10 18 2004 11 59 33 36 5 mins 21909 10 18 2004 12 43 57 11 secs 105 Select All 10 18 2004 12 44 10 6 secs 10 18 2004 12 44 27 43 secs Use Shift click to select groups of casts Ctrl click to select or deselect individual casts Base File Name C Documents and Settings Administratori My Documents Browse Create calibrated data dat files raw files are always stored Close After the directory is loaded select the cast or casts you wish to retrieve e Enter a base file name for the downloaded files The cast number will be appended to this base name to create a unique name for each cast you download If necessary click Browse and select a destination directory for the downloaded files
46. tton adjusts the scales to exactly fit the entire data set This is not subject to the limitations imposed on axis auto scaling described under 6 3 1 At any time you can drag zoom that is click and drag the mouse pointer in the graph area to define a rectangle When you release the mouse the axis 20 limits will be set to the boundaries of that rectangle One of the quickest ways to navigate in a dataset is to first use Auto Scale to show all the data then drag zoom to expand the subset of interest After changing the scaling using one of the zoom commands or drag zoom you can use the Previous Zoom command or button to undo the changes 6 4 Data Markers 3 Graph Properties Graph amp Grid Data Markers Scales Data Marker On Off Color Style Marker Size lade 2 0 circle Line Width ke 2 gt gt cre gt gt Save 5 Defauits Recall Defaults OK Apply Close The properties in this tab control the color marker style and marker size of each data series up to 8 in the graph 51 I I lt I I 4 e To change the color click on the color block and select a color from the subsequent dialog If you select Auto the color will automatically be set to match the wavelength of the corresponding instrument channel To change the marker style select style from the Marker Style combo box change the marker size
47. ydroSoft always saves raw data and gives you the choice of whether to save calibrated data simultaneously HydroSoft stores data directly to disk whenever a data file is open even if it is a new untitled file Therefore the size of the files you collect is limited by your disk space rather than your RAM and you are less likely to lose data in the event of a computer crash The number of data points you can display in a plot is limited by RAM but this limit does not affect the corresponding data files 8 1 Raw Data Raw data files contain a literal record of every byte received from an instrument during the time the file is open Depending on the instrument type and its configuration this may consist of hexadecimal numbers decimal numbers text messages binary data or a mixture thereof HydroSoft adds a header at the beginning of the file with some information about its origin and history but applies no formatting whatsoever to the main data HydroSoft normally names raw data files with the extension RAW 8 2 Calibrated Data HydroSoft normally names calibrated data files with the extension DAT Calibrated data files start with a header identifying the origin and type of the data followed by lines of comma separated values Below is a sample from a HydroScat 2 data file The heading SigmaParams signals the start of parameters relating to the sigma correction which is described in section 7 4 The parameters after the head
48. ydroSoft will open one and will prompt you to name it if the Request user to name files when they are created preference 15 selected also see 10 1 6 Note that it is the instrument not HydroSoft that determines the pace of data collection once it has been started Therefore there may be a delay before data actually appear If set for burst mode the instrument may even put itself to sleep periodically See section 5 3 for information about sampling options When HydroSoft detects incoming data it makes the button visible and changes the title of the Start menu option to Stop 5 3 Setting Sampling Options To set the sampling rate and other parameters of a connected instrument select Sampling Options from the Instrument menu The Sampling Options dialog presents parameters that vary somewhat depending on the type of instrument and on the instrument s configuration The example at left below shows the options for an a Beta or c Beta the example at right corresponds to HydroScat 2 or HydroScat 4 HydroScat 6 s have additional settings relating to their time shared fluorescence channels Further items may appear if your instrument is equipped with an anti fouling shutter or other optional equipment 13 Sampling Options Basic Sampling Sample Rate 503 per second Sample Period 1 33 seconds Start Delay seconds C Decimal Raw data format Hexadecimal Burst Mode Burst mode on Sampling Options
49. ype serial number and other attributes of the currently connected instrument if any 10 3 Processing Menu 10 3 1 View Calibration Opens a dialog box that displays all settings of the current calibration file You can also edit the values in this dialog box For more information see section TE 10 3 2 Select Calibration Opens a standard file selection dialog in which you can designate which calibration file will be used in the current window See section 7 for details about calibration files Once you select a calibration file using this command that file becomes the default for subsequently opened windows If the current window shows data from 44 raw file the data will be recalculated using the newly selected calibration file This does not effect windows other than the one from which the command was executed 10 3 3 Save Calibration File Opens a Save As dialog box with which you can select the name and location for a copy of the current calibration file to be saved 10 3 4 Compare Calibrations Opens a dialog box that displays two calibrations side by side and their differences The first calibration is the one that is in effect in the current window You select the second by clicking the Select Cal 2 button 10 3 5 Process Raw Files Opens a dialog box through which you can convert raw data files in batch fashion to calibrated or raw decimal files See section 9 1 for complete details 10 3 6 Backscattering
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