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HydroRad User`s Manual - Hobi Instrument Services

1. By default the settings specified in the FiltParams command are used FilterType can be 0 1 or 2 A value of 0 zero or off specifies no filtering A value of 1 specifies boxcar averaging in which case each pixel in the output spectrum will be the result of an equally weighted average of the number of pixels or wavelength range specified by FilterSize rounded up to an odd integer if necessary A value of 2 specifies Gaussian averaging where each pixel in the output spectrum will be the result of an normal distribution weighted average with a full width at half max FWHM equal to the number of pixels or wavelength range specified by FilterSize By default the FilterSpec setting specified in the FiltParams command is used If FilterSize is a positive integer then it will correspond to that fixed number of pixels If FilterSize is a negative integer then the filter width will be that many 10ths of nm wide So a FilterSize of 5 specifies a 5 pixel wide filter A filter size of 15 specifies a 1 5 nm wide filter By default the FilterSize setting specified in the FiltParams command is used 8 4 9 LOGAUTO Count SECONDS Average BaseName Process The LogAuto command has been deprecated see Acquire and Log Commands Also note that in version 1 29 the default mode has switched from a minimum duration in seconds to a count LOGAUTO collects data from all enabled channels repeating the collection the number of times specified in C
2. Note that if the battery charger is connected as the only power source operating HydroRad will reduce the charging current to the battery and increase the needed charging time The HydroRad communicates via RS 232 through a standard computer serial port Power and data lines are brought out on a SubConn MCBH8M connector mate MCILSF with pins assigned as shown below PIN FUNCTION 1 Supply voltage 10 to 15 VDC Common RS232 Instrument Receive RS232 Instrument Transmit Battery charging input 18 to 24 VDC Output to Shutter Output to Shutter Short to Common to Disable Battery The supplied cable splits into a DB9 for communication a barrel connector for the battery charger and a pigtail for an external DC supply 15 5 1 Optional Shutter Connector HydroRads may also be configured with a separate MCBH2F connector to drive shutters in which case Pins and 2 are wired to the signals that would otherwise go to pins 6 and 7 respectively on the 8 pin connector 5 2 Optional Daisy chain Connector An MCBHSF connector may be installed through which two HydroRads may be connected to together such that they function as a unit The most common application for this is to connect an instrument measuring irradiance on the surface with one measuring underwater Also see the DAISYCHAIN command in section 8 2 4 5 3 Internal Battery The standard Hyd
3. TEST2 BIN TESTA and TESTT X all match TEST12 DAT does not DEL presents a list of files meeting that file specification and their sizes then asks Delete all the above files If you press Y it will immediately delete them Pressing any other key will abort the command 8 5 5 DIR Filespec Lists all the files on the flash disk whose filenames are described by Filespec Filespec can contain MS DOS wild cards such as and 8 5 6 ERASE Filename Synonymous with DEL Filename 8 5 7 REN OldName NewName Renames the file called OldName to NewName 8 5 8 TYPE Filename Textmode ShowNames Delay Transmits the contents of the file named Filename via the serial port Filename can contain wildcards If Textmode is specified as 1 or on default then Carriage Returns and Line Feeds will be expanded to Carriage Return Line Feed combinations If Textmode is specified as 0 or off then the output will be pure binary If ShowNames is specified as 1 or on default off then filename s precede the output from each file If Delay is specified then the HydroRad waits Delay milliseconds before displaying the output 8 5 9 XS Q X C Filename Initiates an XMODEM send from the HydroRad It is expected that the user will instruct the host computer to receive It should synchronize with hosts that support original 128 byte block XMODEM CRC and 1k XMODEM Original XMODEM can be force
4. following day It will repeat this cycle daily until instructed to do otherwise 9 9 TIMED EXAMPLE 2 intparams 20 1000 0 00 logrange 20 1000 2 6 00 logauto 300 SECONDS 7 00 8 00 9 00 10 00 11 00 12 00 logfixed 10000 Note that example 2 starts with an untimed line Untimed lines that appear before the first timed line are executed only once each time the file is opened whereas timed commands are repeated each day Once all the untimed lines are done the program waits 51 for the first timed line whose time has not yet past So if you were to start this file at 5 00 it would execute intparams 20 1000 then wait until 6 00 and do that line Lines that have a time but no command will repeat the last command that appears before it in the file If you started example 2 at 8 30 it would do the untimed line then at 9 00 it would do LOGAUTO 300 After doing LOGAUTO 300 at 12 00 in this file then LOGFIXED 10000 HydroRad will sleep until 0 00 the next day then do LOGRANGE 20 1000 2 9 10 REALISTIC TIMED EXAMPLE intparams 20 10000 filtparams 100 1000 10 0 logrange 20 13000 5 Logauto 600 SECONDS O OO OO a oes Hore BE HBH OLOO HOU PDUUNDHO se es oe ee ee ee ee ee ee ee ee ee ee SE OO OF se O OO O OO O OO OOO OO O OO O OO O OO OO OO OO ND ND HHHHHHH BE EH i EE HE VEE EEUE PAP EE N When it is first started this file will do the INTPARAMS and FILTPARAMS commands
5. Bright incandescent lights or sunlight are best for quick testing 13 To set the HydroRad s time and date select Set Date Time from the instrument specific menu 2 2 Connection Troubleshooting 14 If there is no response from the instrument try toggling the sleep wake switch a few times This should cause the indicator light to alternate between green to off 15 If the indicator light turns red the sample switch likely needs to be pushed out Once the switch is pushed out the red light should go out in a few seconds 16 If RadSoft cannot connect or if garbage characters are received during either of these operations the baud rate likely needs to be adjusted on the PC 17 If the indicator light is still off the batteries may be either dead or at too low a level to operate the HydroRad s microcontroller properly In this case try charging the HydroRad for a while In some cases it may be necessary to use the battery disconnect plug section 5 3 4 momentarily after charging to revive the microcontroller 18 If the HydroRad will not take a charge be sure to check that the sample switch is pushed out The battery charger cannot simultaneously charge the instrument and provide enough current for sampling 3 OVERVIEW HydroRad is a hyperspectral radiometer that can be configured with up to four channels spectrometers It includes a powerful programmable controller with extensive flash memory and the ability to
6. Ee Ge ee 61 10 10 LOG FILE ONE eeen eea ooi a ea a aea EE 62 11 CUSTOMER SERVICE sees se esse ese esse see ese see see ese ese ese sees se esse See be ese ese See ee SE Seed oge See 63 iv 1 PRECAUTIONS AND MAINTENANCE 1 1 Precautions Handle the fiber optic cables with care Although the jackets are rugged sharp bends can create the risk of breaking the fibers Avoiding bending cables to less than 3 8 cm radius Never lift the instrument by the cables Protect the light collectors Cover them with caps when not in use Use only silicone based lubricants on electrical connectors Do not use acetone or other harsh solvents to clean any part of the instrument Avoid letting the instrument sit in direct sun for prolonged periods If the water temperature is very different from the temperature on deck let the instrument stabilize in the water for 10 minutes before collecting data 1 2 Calibration and Factory Maintenance The HydroRad is a scientific instrument that requires calibration and proper maintenance in order to provide accurate results We strongly recommend returning the HydroRad to HOBI Labs at least annually for testing and calibration by our trained staff using equipment and procedures that are optimized specifically for the HydroRad 1 3 General Cleaning Upon removing the instrument from salt water rinse it thoroughly with fresh water Clean the light collectors before each use with an optical clean
7. PC serial ports do not support 230 400 baud and some may have trouble with even lower rates Also note that high baud rates may not work over long cables If you plan to use high baud rates and long cables in the field test your system first in the lab Changes made with BAUD remain in effect until one of the following events causes HydroRad to return to its default baud rate execution of the RESET command exiting the HydroRad operating program via the QUIT PicoDOS or TOM8 command interruption of power by disabling the battery see section 5 3 4 6 3 CHANGING DEFAULT BAUD RATE You can change the default baud rate by creating an AUTOEXEC BAT file containing a BAUD command on the flash disk This file will be executed each time the HydroRad operating program starts resets or quits to PicoDOS quitting to TOM8 always returns the baud rate to 9600 NOTE before setting a high baud rate as the default test it with the BAUD command If you set the default to a rate that isn t supported well by your computer or cabling it may be very difficult return to a usable rate 19 To create a file setting the baud rate to 57600 note that this process will erase any existing AUTOEXEC BAT file 1 At the HydroRad prompt type CAPTURE AUTOEXEC BAT lt enter gt 2 Atthe capture gt prompt type BAUD 57600 Q lt enter gt lt control z gt You can delete AUTOEXEC BAT or capture a new o
8. and select File Connect If you have a CD with the calibration file for this instrument uncheck the Load calibration from Instrument option in the Connect to Instrument dialog box Click the Find port amp baud rate button or if you know the port and baud rate you could also select the appropriate values and click the Connect button Press the Connect button If this is the first time you have connected to the instrument and you unchecked the Load calibration from Instrument option above you will see a message like RadSoft Must select a calibration File For HydroR ad HR990711 When you click OK you will be presented with the standard Windows dialog box for selecting a file Navigate to the CD containing the calibration file for your instrument and select it 10 When the connection is complete and the calibration is loaded the dialog box should disappear and an icon labeled with the serial number of your instrument should appear on the RadSoft Desktop i HR990711 11 If RadSoft cannot connect see the following section for troubleshooting tips 12 To do a quick check of the HydroRad s functions expose all its collectors to continuous light and select Acquire One Sample from the RadSoft File menu which will collect one sample and display it in a graph on the screen If the light levels on the collectors are low a number of seconds may pass while the instrument seeks the correct integration time
9. bad data or does not reply for 2 seconds the HydroRad will re transmit the data up to 10 times 10 8 STANDARD BINARY FILE FORMAT Standard Binary files can be converted to ASCII files with RadSoft after being transferred to a PC Standard Binary files begin with two lines of text in the same format as ASCII files The first line indicates the model and serial number of the instrument that generated it 60 The second line indicates the channel the name of the channel and the units of calibrated data produced by the channel The name and units may not be included if raw data are recorded Spectra in standard binary files contain the same data in the same order as ASCII files with the addition of a pair of tag bytes The data sequence is as follows OFFO 2 bytes OxOF and OxFO lt RawTime gt 4 byte integer lt Temp gt 4 byte IEEE floating point lt Voltage gt 4 byte IEEE floating point lt Depth gt 4 byte IEEE floating point lt Process gt 2 byte integer lt N gt 2 byte integer lt Scale gt 4 byte IEEE floating point lt Do gt 4 byte IEEE floating point lt Dt gt 4 byte IEEE floating point lt IntTime gt 4 byte integer lt FirstPix gt 2 byte integer lt PixInc gt 2 byte signed integer lt PixCount gt 2 byte integer lt Pixel FirstPix gt see below lt Pixel First PixInc gt see below lt Pixel FirstPix PixCoun
10. by the integration time 4 engineering units are returned full calibration OutputFormat controls whether spectra generated by the logging commands LOG LOGFIXED LOGRANGE and LOGAUTO are in ASCII or binary format 2 spectra saved in binary with CRC checksum and host reply BIN extension on files If the output is to the console the data is followed by a Within 2 seconds the host must respond with an acknowledgment of good data Y or an indicator of bad data X If bad data is indicated or no response is received in 2 seconds then the data is re sent up to 10 times per channel 1 spectra saved in binary with CRC checksum BIN extension on files 31 0 spectra saved in binary BIN extension on files 1 spectra saved in text ASC extension on files 2 for backwards compatibility sets OutputFormat to 0 and sets OutputDestination to 2 3 for backwards compatibility sets OutputFormat to 1 and sets OutputDestination to 2 OutputDestination selects where data are output 0 multiple files Channel letter appended to file name 1 single file host console 2 3 host console multiple files 4 host console single files 8 2 16 PARAMS Displays all the settable parameters Similar to typing LOGPARAMS FILTPARAMS AUTOPARAMS and INTPARAMS in succession except that PARAMS can not change any parameter values This is handy if you forget which parameters are available or which command to use
11. collect and store data on an arbitrary schedule When powered by its internal rechargeable batteries HydroRad can operate autonomously for days or weeks Logged data can be downloaded from HydroRad into any laptop or desktop computer with a standard serial communications port 3 1 Spectrometers Each HydroRad channel consists of its own miniature spectrometer The spectrometer disperses incoming light onto a 2048 pixel Charge Coupled Device CCD such that each pixel on the CCD corresponds to a specific optical wavelength When exposed to light the pixels accumulate charge that is proportional to the total energy at their respective wavelengths Under the control of a microprocessor the pixels accumulate charge for a certain integration time At the end of the integration time the charge from each pixel is read out and digitized resulting in an array of numbers that represents the spectrum of the incoming light By varying the integration time of each spectrometer over a range of 20 ms to many seconds HydroRad accommodates a very wide range of light levels The user can set specific integration times for each channel or allow HydroRad to automatically adjust the integration time according to the light levels it detects 3 2 Optical Inputs and Collector Heads HydroRad s optical inputs are fiber optic connectors to which various light collectors can be connected through fiber cables HOBI Labs supplies irradiance and radiance heads for
12. for a particular setting See also SAVEPARAMS LOADPARAMS 8 2 17 PIXEL Channel Wavelength Given a channel and wavelength displays the pixel most closely corresponding to the wavelength Channel may be specified with a letter a number or an asterisk to specify all channels If no channel is specified the current CHAN setting is used 8 2 18 SAVEPARAMS Filename SAVEPARAMS stores all the parameters set with LOGPARMS INTPARAMS AUTOPARAMS and FILTPARAMS in a file with the given Filename If no Filename is specified they will be stored in HYDRORAD INI which is automatically loaded whenever HydroRad starts up 8 2 19 SET VariableName Value Sets the value of environment variable VariableName to Value which can be a string or numeric expression Use VariableName to insert the value into other expressions 32 8 2 20 SHOWCAL Channel FirstPixel LastPixel Displays in ASCII the currently loaded calibration data for a given channel from the FirstPixel to the LastPixel Header information displayed includes HydroRad Serial Number Channel name Units and Scale For each pixel between FirstPixel and LastPixel the constants displayed include F which determines the dark current calibration function to use C which is the floating point constant used in the dark current calibration and Epsilon which the count rate is divided by to obtain engineering units Channel may be entered as a letter a number or an
13. high duty cycle logging Also ASCII files take longer to write to the flash disk possibly slowing the data collection rate 10 10 LOG FILE HydroRad keeps a text file called HYDRORAD LOG on the flash disk that records the dates and times in a human readable form at which it stores data and performs various other actions This can be useful for post analysis of data and troubleshooting The operating software continuously adds to this file so you may wish to delete it occasionally Ifno HYDRORAD LOG exists the operating software will generate a new one 62 11 CUSTOMER SERVICE For technical support or questions about your instrument contact our technical support department at support hobilabs com or call our main office If your HydroRad needs to be returned to HOBI Labs for repair maintenance or calibration contact HOBI Labs customer service service hobilabs com or visit the contact page on www hobilabs com and provide the following information Instrument Serial Number Reason for return Method of return Federal Express United Parcel Service etc Contact person Date needed Delivery address HOBI Labs will notify you of estimated cost and turnaround time as soon as possible after receiving the instrument Repairs will not be started until you approve the cost estimate and turnaround time 63
14. not performed by the HydroRad itself with a few exceptions 1 If data files do not contain every pixel within a range that is if you have set FILTPARAMS s Pixellncrement parameter to a value other than 1 it will be impossible to perform the pixel compensation process step 1 2 Spectrally filtering data whose dark offsets have not yet been subtracted can seriously degrade their signal to noise ratio 3 Averaging spectra processed to a level less than 3 can degrade their accuracy although the effect may not be severe if the range of integration times included in the average is modest For most purposes we recommend you perform no processing on the HydroRad except possibly to limit the range of pixels saved That is select level 0 use no averaging or filtering and set the Pixellncrement parameter of FILTPARAMS to 1 Saving complete raw spectra gives the most flexibility and accuracy for later processing with RadSoft or other software Raw binary files also produce the most compact possible data files pixel for pixel However if you process and filter the spectra in situ you may be able to save a smaller set of pixels and reduce the overall file size see 10 9 The computation time required for processing varies widely depending on the settings of various parameters from a small fraction of a second to several seconds per spectrum If your application requires collecting spectra in rapid succession you may wish to store raw data
15. of pixels using the Pixellncrement parameter of INTPARAMS you should select a processing level of 1 or higher so that step 1 will be performed in situ before the pixels are selected 10 1 2 Process 2 Dark Offset Subtraction Each pixel in a CCD produces a characteristic offset which is a function of temperature and integration time in the absence of light HOBI Labs measures the offsets over a wide range of conditions then distills this information into a set of parameters for each pixel Processing step 2 is to calculate and subtract this offset from the measured signals 10 1 3 Process 3 Time Normalization CCDs are inherently integrating and their output is proportional to the energy accumulated during their integration time However most applications call for a measure of power such as irradiance or radiance Step 3 is to divide the measured signal by the integration time to convert from energy to average power 53 10 1 4 Process 4 Spectral Normalization and Units Conversion Based on measurements with a well calibrated standard light source step 4 compensates for the non uniform spectral response of the CCD and other optical components and converts the measured spectra to engineering units 10 2 CHOOSING THE PROCESSING LEVEL The level of processing applied by the HydroRad is set by the processing parameter of the LOGPARAMS command see 8 2 15 In most cases RadSoft can also subsequently perform any processing steps
16. on a flat surface On the HydroRad this means the end cap on the opposite end from the connector endcap HydroRad Total Channels Fiber Optic Embedded Model spectrometers Collectors Collectors 1 1 1 z E1 1 1 ES1 l 1 with anti fouling shutter 2 2 2 E2 2 2 one on each end 3 3 3 4 4 4 Type Diameter Length Dry weight Submerged weight HR 1 and 13 3 cm 30 5 cm 3 3 kg 0 5 kg 2 5 25 12 HR 3 and 13 3 cm 46 6 cm 5 3 kg 1 kg 4 5 25 18 3 HydroRad E1 with a plane irradiance collector and HydroRad 2 with one plane irradiance and one radiance collector 10 cables Connector endcap of a HydroRad 3 E and L collectors 11 HydroRad E2 Endcap with embedded Radiance Collector Note that any cable attached to the electrical connector must be kept out of the field of view of the collector 15 or less 4 2 Spectrometer Configurations and Performance The spectrometers within each HydroRad can also be configured with various options The key variable components in the system are the diffraction grating which determines the spectral sensitivity curve and the entrance slit which offers a tradeoff between sensitivity and spectral resolution Most HydroRads are configured with 50 micron slits which provide spectral resolution of less than 3nm FWHM and good sensitivity see the discussion of sensitivity
17. then wait for the next listed hour to start It will collect 10 minutes 600 seconds of data every hour during daylight hours and a range of dark integrations every midnight 52 10 DATA PROCESSING AND STORAGE 10 1 CALIBRATION PROCESSING STEPS HydroRad s operating software can save data in raw form as fully calibrated engineering data or in any of several intermediate stages of processing The same processing and more can also be performed by the RadSoft Windows software after data have been transferred from the HydroRad to a computer The stages in processing are described below These steps are always performed in sequence all the steps up to and including that specified by the LOGPARAMS command are performed before data are saved in files In addition multiple spectra may be averaged see 8 4 9 8 4 10 8 4 11 and spectral filtering applied see 8 2 7 after the specified processing 10 1 1 Process 1 Pixel Compensation Step 1 uses information from adjacent pixels to compensate for pixels that are identified during calibration as more unpredictable than others A small but significant percentage of such pixels are found in most CCD chips This process may result in a small shift in effective wavelength for these pixels The worst case shift is equivalent to 2 pixels or about 0 6nm IMPORTANT This process can only work when every pixel within the desired spectral range is available Therefore if you plan to select a subset
18. with a slave HydroRad have MaxChan values greater than the number of local spectrometers to account for additional slave spectrometers Slave HydroRads to be attached to a master HydroRad have BaseChan values that are one greater than the number of channels on the master So if a HydroRad 1 and a HydroRad 2 were to be daisy chained together one would enter on the master unit HydroRad 1 DaisyChain A C And on the slave unit HydroRad 2 DaisyChain B C Once this is done the slave unit will start saving logged data to files with the B and C suffixes instead of A and B Also slave units normally have ECHO set to off to streamline the master slave communications Setting slave units echo setting to on can have unpredictable effects See the ECHO command for more information 8 2 5 DEPTHCAL Offset ScaleFactor DEPTHCAL sets the coefficients used to calculate calibrated depth readings from the HydroRad pressure sensor Offset is the raw reading at atmospheric pressure ScaleFactor is the coefficient to convert digital counts to equivalent meters of depth in water Values entered with DEPTHCAL take effect immediately and are saved in the file DEPTH CAL so they will remain in effect until changed with another DEPTHCAL command 28 8 2 6 DATE mm dd yy hh mm ss Identical to the TIME command Sets the date and or time of the real time clock The command will accept partial dates for example 3 1 sets the month t
19. A FILES HydroRad saves spectra collected with the LOGAUTO LOGFIXED and LOGRANGE commands in files on the flash disk which can be downloaded via the serial connection to a PC see section 6 4 Files are assigned a base name of up to 7 characters to which HydroRad appends a letter indicating to which channel it corresponds A for channel 1 B for channel 2 etc and an extension indicating whether the file contains binary or ASCII data BIN and asc respectively For example a base name of hydro on a HydroRad 3 will result in files named hydroA ASC hydroB ASC and hydroc Asc containing data from the three channels The base name may be entered as part of the command see the descriptions of LOGAUTO LOGFIXED and LOGRANGE for details If no base name is specified a name will be formed from the current date in the form YYMMDD All the spectra saved at any time on a given date are stored in the files named for that date In the unlikely event the integration time actually starts in one day and ends in the next the spectrum will be saved under the later date Data assigned to files that already exist are always appended to the existing file Files may be stored in binary or ASCII format The format is set with the LOGPARAMS command and defaults to ASCII 10 6 ASCII FILE FORMAT The first line of each data file indicates the model and serial number of the instrument that generated it The second line indicates the channel the
20. Donigh Dt time variant Dark Offset Average Signal from Pixels Dtjoy to Dtrign DarkCorrection Pixel Do C pixel Dt Do FixedSignal Pixel FixFunction Signal Pixel F Pixel Corrected Pixel FixedSignal Pixel Dark Correction Pixel LinearityAdjusted Pixel Corrected Pixel Adjustment Corrected Pixel Rate Pixel Linearity Adjusted Pixel Integration Time Offset EngineerngUnits Pixel e pixel Immersion Pixel Rate Pixel Scale Wavelength WotPixel W Pixel W2 10 4 1 Identification This section identifies the instrument to which the calibration belongs The first line after the label is taken as the serial number of the instrument The firmware compares this to the serial number of the HydroRad and warns the user if it s different The next line is the configuration string Example ID HR990501 CD4S50L2 55 10 4 2 Channel Information Dark Correction Epsilon and Immersion Correction This section begins with the channel letter in brackets such as A for the first channel The firmware only looks for letters A through D Line 1 after the marker contains a string of up to 31 characters that gives the real name of the channel For example Irradiance_down or Radiance up At this time these strings cannot contain spaces Line 2 contains the units of the calibrated data e g W m 2 nm or W m 2 nm sr Line 3 gives an overall scale factor which is applied to all the data i
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22. HydroRad Series 300 Multi Channel Hyperspectral Radiometers User s Manual Version 300 A HOBIL Abs Hydro Optics Biology amp Instrumentation N Laboratories A Lighting the Way in Aquatic Science d y www hobilabs com support hobilabs com Revisions Version 300 A December 2011 Eliminate portions specific to series 200 instruments Expand Precautions and Maintenance section 1 Minor corrections and formatting Version 1 33g November 2007 Update layout diagrams section 2 add switch diagrams section 7 Change references to HydroRad D2 to HydroRad E2 section 4 Update battery endurances section 5 3 1 Version 1 33f June 2006 Add picture of HydroRad D2 name changed to E2 in rev 1 33g note about models without batteries Version 1 33e June 2005 Correct power consumption section 5 Delete HyperTerminal XMODEM and YMODEM from section 6 Version 1 33d May 2005 Add pin diagram section 5 Version 1 33c April 2004 Improve descriptions of configurations including optional shutter and daisy chain connectors and spectrometer performance Change DD cable to PDP Version 1 33b March 1 2004 Correct obsolete references to HRCal in section 9 Version 1 33a February 9 2004 Correct obsolete reference to the operation of the trigger switch in section 9 3 Version 1 33 September 25 2003 Added limited firmware support for HydroRads without flash memory Eliminated user sele
23. N sees se esse sees see see se Ge SEE Be EE SERE Be EE SEE EE EE EE RA Se EE SEE Be Ee Ee Ee 36 8 5 FILE OPERATIONS ese seesse esse ees ee sees se ee sees Se ee Ee SEE Be ee SEE Dee ee Ee SEE Be Ee SEE Be Se ee Ee 45 8 6 AUXILLARY SERIAL PORT COMMANDS ee sees se esse ese esse sees se esse ss ee be ese ese es ge See se ee se 47 8 7 DEBUGGING AND TESTING ueeseesse esse see sees se ee GEE SEE Ee Ge EE SEE Be EE RE Be Ee Ee EE Ge Ee ee ge ee 47 8 8 HELP scscsssssssssssrscesceccscsscssssenecsecssnsneeseesecssnsscssecsscsesscosenecsesssneseesecsscsecssessecssnsssseessess 48 9 COMMAND EFILEG scrcccsserssrsssscesserssrssssseessessessesssecsesssnssessesssesossscssecssessessecssessesses 49 9 1 GENERAL FORMAT ccccscscssssscssecsscsssscnecscsesssnsnessecsscsecssessscsscssssenecsessesssnssessesseesees 49 9 2 SIMPLE EXAMPLE esse sees se esse se sees sees se es ee sees se ese ee See Be ee See Bee Be ee SEGE ee EE Ge Ee Re Se ee ee 49 9 3 TRIGGER CMD EXAMPLE esse sees se esse ese see sees se ese sees be esse See See Be ee SEGE Dee Ee EE Ge Re Se ee ee 49 9 4 TIMED COMMAND FILE FORMAT scsssssssssscsssssssssssssssssesecsesssrsscesesssssrssessoesses 50 9 5 EXECUTION GEE ee ne 50 9 6 HALTING EXECUTION cccssssssssssssssesscsscssssssscssecsscssesssecsesscssssesecsesssnssessesseeseesees 50 9 7 TESTING aaee eeaeee e aa See EE TEOS EESE A SEA 51 9 8 TIMED EXAMPLE 1 see sees sesse esse sees se esse s
24. Rad is configured as a virtual hard disk with a standard capacity of 48 Megabytes and optional capacities from 15 up to 256 Megabytes The flash disk supports a file system like that found on desktop computers which allows the user to manage files using familiar commands like erase copy dir for directory and ren for rename RadSoft extends the user interface to the Windows world allowing the user to manipulate files with a familiar Explorer like interface HydroRad offers various options for processing spectra before storing them It can store data in raw partially calibrated or fully calibrated form average multiple spectra and apply spectral filtering 4 _HYDRORAD CONFIGURATIONS The HydroRad family comprises a range of configurations including different numbers of spectrometers spectrometer setups and collector configurations 4 1 Base Models The number in the HydroRad model indicates how many channels spectrometers it contains For each channel the default configurations include one collector mounted on a fiber optic cable Collectors may also be embedded that is mounted directly on the HydroRad housing with no external fiber optic cable This is most commonly used for a surface mounted units that measure irradiance above the water surface but also provides a convenient all in one package for other applications Since irradiance collectors pick up light from all angles they must be mounted
25. TUP New in firmware 1 26 Shows the configuration of the NMEA output auxiliary device if one is attached 8 2 3 BAUD newrate Q Change to a new baud rate Without the Q flag BAUD replies Changing to XXXX BAUD Hit lt return gt when ready and waits until it receives another character not necessarily lt return gt With the Q flag which stands for quiet the baud rate will immediately change without any further input There must be a space between the newrate parameter and the Q flag or the Q will be ignored 27 Standard baud rates from 300 to 230 400 baud are supported Note that most PC serial ports do not support 230 400 baud and some may have trouble with even lower rates Also note that high baud rates may not work over long cables If you plan to use high baud rates and long cables in the field test your system first in the lab The baud rate you set remains in effect until changed by another BAUD command you exit the HydroRad operating software or the HydroRad is reset by removal of power or the RESET command See also sections 6 2 and 6 3 8 2 4 DAISYCHAIN BaseChan MaxChan New in firmware 1 25 For daisy chained HydroRads this command controls the master slave relationships and the numbering of channels For non daisy chained HydroRads BaseChan is set to channel A and MaxChan is set to the maximum available channel on the HydroRad B for a HydroRad 2 for example Master HydroRads
26. annel Displays a crude graph of the most recent raw spectrum whose numerical values can be viewed with RAW The X axis represents pixels numbers over the range specified by FirstPixel and LastPixel The width of the graph is fixed at 80 characters If no FirstPixel and or LastPixel are specified the corresponding values set by the FILTPARAMS command will be used The Y axis represents pixel amplitudes in digital counts VerticalScale specifies the graph s height in lines The Y axis always covers the full range of pixel values from 0 to 32767 Therefore the default VerticalScale value of 32 is equivalent to 1000 counts per line 38 If Channel is specified or an asterisk for all channels the most recent spectrum from that channel is shown Note that because of the low resolution of the display many details of the spectrum may not be apparent 8 4 7 INT Channel Time Collects a spectrum from the specified Channel with the specified integration Time in ms Channel may be entered as a letter a number or an asterisk to indicate all channels If no Channel is specified uses the most recently specified channel that displayed by CHAN If no Time is specified uses the time most recently used by the current or specified channel The Time parameter may also take the form of Time Time Time or Time In this case the operator specified and the new Time argument will be applied to the previous integration time for th
27. ark current compensation 3 normalized by integration time 4 engineering unit scaling full calibration A pair of control c characters received via the serial port during execution of LOGFIXED will abort the process 43 8 4 11 LOGRANGE MinTime MaxTime TimeStep Mode Averages BaseName Process LOGRANGE repeatedly executes LOGFIXED over a range of integration times The first integration on each channel will be for MinTime milliseconds If Mode is 1 the second integration will be at MinTime TimeStep If Mode is 0 zero the second will be at MinTime TimeStep Integrations continue with increasing length until the integration time is equal to MaxTime If the last calculated time is greater than MaxTime a final integration will be performed for MaxTime For example LOGRANGE 20 1000 3 1 will integrate each channel at 20 60 180 540 and 1000 milliseconds If MinTime MaxTime or TimeStep is omitted the corresponding value set by INTPARAMS will be used Averages and BaseName have the same meaning as with LOGFIXED IMPORTANT See section 10 2 for information about how averaging can affect the quality of your data If a value is specified for Process this value will override the Processing value set up with the LogParams command This parameter controls which calibration steps are applied to data before they are filtered and saved 0 raw unprocessed 1 weak pixel adjustments 2 dark current compensation 3 normali
28. asterisk to indicate all channels 8 2 21 TIME mm dd yy hh mm ss Identical to the DATE command Sets the date and or time of the real time clock The command will accept partial dates for example 3 1 sets the month to 3 and the day to 1 without affecting the year and times for example 13 24 sets the hour and minute without affecting the seconds Years may be entered with 2 or 4 digits 8 2 22 TXDELAY Delay Sets the minimum time in milliseconds by which HydroRad delays its responses to commands in case the system with which it is communicating requires such a delay 8 2 23 VER Displays the version number and date of the HydroRad firmware 8 2 24 ZERODEPTH ZERODEPTH measures the current raw reading of the pressure transducer then records this as the Offset used for calculations of calibrated depth which may also be set with DEPTHCAL If executed while the HydroRad is at atmospheric pressure ZERODEPTH compensates for offset errors due to the effects on the transducer of temperature and barometric pressure 8 3 GENERAL OPERATIONS 8 3 1 lt enter gt Pressing the enter key on a blank line will repeat the last command 8 3 2 command Any command preceded by an asterisk will be passed to the slave unit if any for execution In this manner you can send commands to a slave unit without executing the command to the master unit This is not needed under normal circumstances 33 8 3 3 command Any com
29. ata collected at that optimum exposure even if other channels need to try other integration times If QuickAuto is disabled zero or off then all channels continue to collect new data until all channels have optimum exposure Execute Cancel Hide Help Pressing Execute after filling in the desired fields sends the correctly formatted command to the HydroRad 8 1 2 HydroRad Reserved Words The words on open or yes are all defined as equal to 1 in command arguments that expect logical values and may be used in place of the value 1 In place of the value zero in command arguments the words off close or no may be used These words are not case sensitive 8 1 3 HydroRad Channel Numbering Commands that refer to channels will accept either a channel number or letter as an argument Thus the first channel can be referred to as either 1 a or A 8 2 CONFIGURATION COMMANDS 8 2 1 AUTOPARAMS SatValue MinPeak MaxSatPixels MinPeakPixels MaxAttempts PreFilter Shows and sets parameters governing the automatic setting of integration time used by AUTO ACQUIRE LOG and LOGAUTO The first four parameters define what is considered an acceptable dynamic range for the pixel values in a spectrum SatValue defines the value at which a pixel is 26 considered saturated MinPeak is the minimum value at which a pixel is considered fully exposed The range for both of thes
30. ata collection The trigger switch has no effect if the sensor is asleep However if the trigger switch is turned on while the sensor is asleep it will cause a trigger event when the 23 instrument wakes Also if collection was started with the trigger switch in the on position and the trigger switch is shut off while the instrument is asleep then collection will halt when the instrument wakes HydroRad Switch Locations Sleep Wake Switch show in sleep position Dec 8 EE O O AN N ST NG o 3 NO A A K Trigger Switch shown in off position 24 8 COMMANDS HydroRad is controlled and configured with text commands received via its serial port Its commands are designed to be human readable and reply with informative messages although they could also be generated from a user programmed computer or logger All commands can also be executed from files stored in HydroRad s flash memory see section 9 8 1 COMMAND CONVENTIONS For clarity in this document commands are shown in upper case but they are not case sensitive Some commands accept arguments which are separated from the base command and from each other by commas or spaces Arguments may be individually omitted in which case they will have no effect For example if a command accepts three arguments in the form COMMAND argl arg2 arg3 or COMMAND argl arg2 arg3 you may adjust only arg3 by
31. below If the utmost sensitivity is required 100 or 200 micron slits are also available but these will degrade the spectral resolution Depending on the collector configuration fiber optics larger than our standard 200 micron may be available to increase the sensitivity also If resolution is more important than sensitivity smaller slits can be used The diffraction grating is the most important variable in determining system spectral response The sensitivity of the CCD detector is also crucial but cannot be changed Most HydroRads are supplied with a standard grating that provides a usable spectral range of approximately 350 to 850 nm The spectrometer response falls gradually at both ends of the spectrum so there are no distinct cutoff wavelengths The 12 effective spectral range of the system depends on the application and the ultimate sensitivity signal to noise ratio and dynamic range required To understand this better see the following plot The plot shows the complete system response for a spectrometer with a planar irradiance collector 2 meter 200 micron core fiber optic cable and 50 micron entrance slit The upper curve is the irradiances at which the spectrometer saturates when operating at its minimum integration time The lower curve show the effective noise irradiance within 10nm bandwidth averaging when the integration time is set to 20 seconds The curves have the same shape indicating that the noise level is a cons
32. cates that channels 1 and 3 are enabled Note that HydroRads may be equipped with different numbers of channels Normally all installed channels should be enabled 30 8 2 12 LAMBDA Channel Pixel Given a channel and pixel ranging from 0 to 2047 displays the wavelength in nm corresponding to the pixel Channel may be specified with a letter a number and asterisk for all channels If no channel is specified the current CHAN setting is used 8 2 13 LOADFILT FileName Eliminated in firmware version 1 29 8 2 14 _LOADPARAMS FileName LOADPARAMS restores parameters saved in a file by SAVEPARAMS If no FileName is specified it loads HYDRORAD INI 8 2 15 LOGPARAMS Samplelnterval SampleDuration Processing OutputFormat OutputDestination Samplelnterval and SampleDuration both in seconds are used for continuous periodic collection as initiated by the START command or trigger switch They are not relevant to collection scheduled by a command file unless that file contains a START command IMPORTANT See section 10 2 for information about how the Processing parameter can interact with other parameters to affect the quality of your data The Processing parameter controls which calibration steps are applied to data before they are filtered and saved 0 raw unprocessed counts are returned 1 weak pixel adjustments are performed 2 dark current is calculated and subtracted from the counts 3 counts are divided
33. ction of QuickAuto mode Expanded discussion of Auto integration parameters in section 8 2 1 Version 1 31 August 1 2003 Major overhaul in all sections to accommodate Series 300 HydroRads and RadSoft Major change in the operation of the LogAuto command see section 8 4 9 Added description of Binary CRC and Prompted CRC data formats in 10 7 Major change in the operation of the Trigger switch see section 7 2 Eliminated section 11 HRCAL Version 1 232a February 19 2002 Revised HyperTerminal and section 11 Windows Drag Drop Mode Version 1 232 October 10 2001 Start of revision tracking ii 1 PRECAUTIONS AND MAINTENANCE ccssssssssssorsrsvessessesvsnssessscsscssessesseessesssneeess 1 Tels PreCautiOs ssiscccsssccnesissscescssssnsssososventeedenescedsnsevecnsnndecsasecuccecacecccecseatccccceseeeceaetecssomsteccceseesedens 1 1 2 Calibration and Factory Maintenance sesse esse es soe esse ee Ee Ee EG EG Ge Ge BE Ge Se Ge EE ge 1 1 3 General Cleanio sis esdseses ese d so sd soe eo Dek Se eo ee No ee Ge sd eo od de eg De Ee Go N do rs de ge eg 1 1 4 Pressure TransduCei is sissies ss ed sccescavocsetcsuseedeeccssesdeteceeseesseesensstsececonesegesbabegescecssecse 1 1 5 Electrical Coinnietdrs issie sesde deels see see seges doe sed see ge ie iese dd oe eke di ene eke ede de 2 1 6 Mounting and Deployment esse esse soe esse ee se ee BE Ge Ge EG Ee EG EG EG GE ee DE Ge SG Ge Go EE Ge ee 2 L7 ou ER EE
34. d PixIncrement will correspond to physical pixels If PixInc 1s a negative number and a calibration has been imported into the HydroRad see ImportCal then FirstPix and LastPix and PixInc will be 10ths of nanometers For example if 400 2000 and 2 are specified then the output will consist of pixels 400 402 404 406 2000 If 3500 8500 and 25 are specified then output will consist of pixels corresponding to wavelengths at 350nm 352 5nm 355nm 357 5nm 850nm By default FirstPix 1 LastPix 2047 PixInc 1 corresponding to every pixel FilterType can be 0 1 or 2 A value of 0 zero or off specifies no filtering A value of 1 specifies boxcar averaging in which case each pixel in the output spectrum will be the result of an equally weighted average of the number of pixels or wavelength range specified by FilterSize rounded up to an odd integer if necessary A value of 2 specifies Gaussian averaging where each pixel in the output spectrum will be the result of an normal distribution weighted average with a full width at half max FWHM equal to the number of pixels or wavelength range specified by FilterSize By default FilterType is 0 and FilterSize is 1 no filtering 37 If FilterSize is a positive integer then it will correspond to that fixed number of pixels If FilterSize is a negative integer then the filter width will be that many 10ths of nm wide So a FilterSize of 5 specifies a 5 pixel wide filter A filte
35. d with the X option or XMODEM 128CRC with the C option The Q option inhibits messages To cancel a pending transfer press lt contro1 x gt several times 8 5 10 XR Q X C FileName Prepares HydroRad to receive an XMODEM transfer It is expected that the user will instruct the host computer to send It should synchronize with hosts that support 46 original 128 byte block XMODEM CRC and 1k XMODEM Original XMODEM ca be forced with the X option or XMODEM 128CRC with the C option The Q option inhibits messages To cancel a pending transfer press lt contro1 x gt several times 8 5 11 YS Q G FileSpec Initiates a batch file send using the YMODEM protocol Sends all files whose filenames match FileSpec which can contain DOS wildcards such as or 2 YS can be forced to YMODEM G no error checking recovery with the G option The Q option inhibits messages To cancel a pending transfer press lt control x gt several times 8 5 12 YR Q G Initiates a batch file receive with automatic file naming using the YMODEM protocol YR can be forced to YMODEMG no error checking recovery with the G option The Q option inhibits messages To cancel a pending transfer press lt control X gt several times 8 6 AUXILLARY SERIAL PORT COMMANDS 8 6 1 SERCLOSE Closes the 2nd serial port Not implemented on all systems 8 6 2 SEROPEN BaudRate Opens the 2nd serial port at the specified baud rate Data r
36. e channel So if the previous integration time for channel A was 35 ms and the command INT A 2 was used channel A would be integrated for 70 milliseconds This may be useful for intentionally overexposing the spectrometer after a AUTO command to get better resolution in the UV in UR ranges 8 4 8 LOG AUTO FIXED Count SEC Average BaseName Process Format Dest Channels FirstPix LastPix Pixinc FilterType FilterSize Collects data from all channels storing the data as specified in the Params settings by default This command is very similar to the ACQUIRE command but uses different default settings The first optional parameter sets the exposure time mode AUTO iteratively tries to find the optimum exposure time for each channel within the limits set with INTPARAMS which may mean that for each data sample the instrument may take several measurements FIXED re uses the last integration time or the times specified in the TIMES command SPEED default uses auto integration for the first data collection and then makes only one measurement per subsequent data collection Occasionally data samples will be over or underexposed but overall the data sampling rate will be maximized The second parameter Count specifies the number of samples to take If the word SECONDS or an abbreviation as short as sec appears as the next argument then Count is to be interpreted as a duration in seconds during which data should be collec
37. e values is 2000 to 32760 Please note that higher SatValue and MinPeak settings will result in more fully saturated potentially more accurate readings when used with the LogAuto Log Auto or Acquire Auto command sequences However when using the Log or Acquire commands in the default speed auto mode higher settings will lead to more over exposed samples and less usable data In fact if light levels are changing rapidly lower SatValue and MinPeak settings will result in fewer over exposed measurements and more usable data in speed auto mode The algorithm will attempt to find an integration time that results in a spectrum that has at least MinPeakPixels whose values are between SatValue and MinPeak It will allow up to MaxSatPixels that exceed SatValue MinPeakPixels has the lowest priority of the criteria A spectrum may be considered well exposed even if it does not meet MinPeakPixels MaxAttempts is the maximum number of trial integrations allowed The algorithm will terminate after this many integrations if it does not achieve a spectrum that meets the dynamic range criteria Within LOGAUTO the last integration will be logged whether or not it terminated normally PreFilter sets the width of a filter that excludes occasional hot pixels from consideration Under most circumstances this should be set to 3 The QuickAuto parameter existed in firmware versions 1 25 through 1 32 but has been eliminated 8 2 2 AUXSE
38. eceived from the 2nd serial port will be sent to the first serial port Not implemented on all systems 8 6 3 SERSEND String Sends string including ANSI escape sequences to the 2nd serial port Not implemented on all systems 8 7 DEBUGGING AND TESTING 8 7 1 FREEMEM Displays the amount of RAM available for debugging 8 7 2 PIXDELAY Used only for testing 47 8 7 3 SIM State Turns on or off simulation mode In simulation mode the actual spectrometer data are ignored and each integration results in a triangular spectrum whose overall amplitude is proportional to the value of State If State is 1 the amplitude will be based on a random value 8 7 4 TEST Used for debugging 8 8 HELP 8 8 1 Command or HELP Command Displays information related to specified command If no command is specified lists available commands 48 9 COMMAND FILES HydroRad commands can be loaded and executed from files stored on its flash card exactly as if they had been received on the serial port from a user By convention these files have the extension cmd and are referred to as command files They are similar to MS DOS batch files with the addition that they may specify a real time schedule for executing commands Most command files are executed by typing the file name of the command file minus the cmD extension Command files can also be executed with the RUNFILE command Upon startup HydroRad will automatically execute the
39. ee see sees se ee See Be ee Se SEE Be ee ERGE ee Ee ee Re Se ee ee 51 9 9 TIMED EXAMPLE 2 uses sees sesse esse sees sees see ee see sees Se ee SEE Be ee SEE SEE Be Ee EE Ge Dee Ee EE Ge Re Se ee ee 51 9 10 REALISTIC TIMED EXAMPLE cscscssssscssessssssssssessessssessssessessssssceseesecssrssesseesses 52 10 DATA PROCESSING AND STORAGE esse esse sees sesse esse see see oge Seg Seg Be SS SEE Be Se SEER ese 53 10 1 CALIBRATION PROCESSING STEPS seesseessesse sees se esse sees see sees se ee See se ee See Se ese 53 10 2 CHOOSING THE PROCESSING LEVEL see sse esse sees se ese esse sees sees se ee see sees se ese See sees see 54 10 3 CALIBRATION FILES esee sesse esse sees see se Se GE Ee SEE Be EE SEE Be Be Ee SEG DEE EE GE SEE RE Se Ee SEE ee Ee 54 10 4 ASCII CALIBRATION FILE FORMAT ees sesse ese esse sees se esse sees se ese ee See Be ee EE Ge ee ee ee 55 10 5 DATA FILES esse sesse sees se ee SEE Be Ee EE SEE Be Ee ERGE BEE EE EE GE SEE Se EE SEER Be Ee RE Be Ee EE GEE Ee Se aS 58 10 6 ASCH FILE FORMAT sesesseseeeeseseeccsoesescesoseeseecsseseeeoseeseeoesossesesoeseeoceoseeseeeesosseeoseeseeoeeos 58 10 7 BINARY CRC amp PROMPTED CRC FILE FORMATS uses sesse sesse esse see sees se esse ese 59 10 8 STANDARD BINARY FILE FORMAT eseesseessesse sees se esse sees sees sesse es ge sees se ee See See se ese 60 10 9 DATA FILE SIZES ee sesse esse sees se ese esse sees Be ee SEE Bee ee EE SEE Se Ee SEER Be Ee RE Dee Ee ERGER Ee
40. entering COMMAND arg3 In firmware versions 1 17 and later combinations of spaces and or a single comma are treated as a single delimiter In previous firmware versions every space or comma was treated as a separate delimiter Most commands reply with the settings of relevant parameters or other status information 8 1 1 Sending Commands from RadSoft If a HydroRad is connected through RadSoft then any of the commands listed in this manual can be sent with the correct syntax i e the correct number of commas though the RadSoft command window for that command Commands may also be typed directly into the RadSoft terminal window Once a HydroRad is connected through RadSoft its device specific menu will be enabled that is the menu with the HydroRad s serial number as its title Within the device specific menu there are several sub menus that reflect the sections that follow in this manual Direct Config Commands Direct General Commands Direct Data Commands etc Within each of those menus are several commands Selecting a command launches a command dialog that displays the command name and includes an edit box of each filed of the command Help information is also displayed to assist the user with filling in the command For example if AutoParams were selected from Direct Config Commands the following dialog would appear 25 AHydroRad AutoParams command afd SatValue MinPeak MaxSatPixels MinPeakPixels MaxAttemp
41. es depending on the command being executed After one or more control C s HydroRad will reply Really abort command cmd Press Control C to confirm If you press lt control c gt again within 4 seconds execution of the command file will end If you press a different key or do not respond with 4 seconds execution will resume 50 9 7 TESTING HydroRad command files are essentially computer programs and it can be surprisingly easy to create bugs in them Before deploying a command file of any complexity you should test it to verify it that it behaves as you intend If your file includes long periods of sleep you can accelerate its execution by pressing a key not control C unless you want to halt execution once or twice to wake it from each sleep It will detect that it woke early and display the message sleep interrupted but will nevertheless continue with the next command then sleep until the next scheduled time You can also interrupt time consuming LOGAUTO LOGFIXED and LOGRANGE commands without halting file execution by pressing lt control c gt once during the command 9 8 TIMED EXAMPLE 1 20 00 logauto 600 21 00 logauto 600 22 00 logauto 300 logfixed 10000 23 30 logfixed 100 This file will do LOGAUTO 600 at 8PM and 9PM Sleeping after it s done each one At 10PM it will do LOGAUTO 300 immediately followed by LOGFIXED 10000 then sleep until 11 30PM and do LOGFIXED 100 Then it will sleep until 8 00 the
42. f an AUTOEXEC BAT file is present on the flash disk it will be executed If the current baud rate is other than 9600 PicoDOS will set it to 9600 unless otherwise instructed in an AUTOEXEC BAT file see also 6 2 and 6 3 8 3 9 POWER State Turns on state 1 or off state 0 power to the spectrometers POWER may also be used without an argument to display the current status Any command that initiates an integration will automatically turn on the power first if necessary and executing SLEEP will turn it off so this is rarely needed in normal use 34 8 3 10 PRESSURE Displays the current raw reading of the pressure transducer See also DEPTH 8 3 11 RESET Reinitializes the HydroRad program which executes any BAUD command in AUTOEXEC BAT if it exists loads the parameters in HyDRORAD INT if it exists executes the commands in HYDRORAD cCMD if it exists and loads any calibration files that exist 8 3 12 RUNFILE FileName Executes a command file named FILENAME CMD See section 9 for a discussion of command files 8 3 13 SETDCHAN Channel State Sets the state of a digital output channel to the value specified in State This command is used mainly for debugging On older HydroRads without shutter electronics Channel 1 underwater connector pin 6 and Channel 2 underwater connector pin 7 State can be either 0 or 1 8 3 14 SLEEP Seconds Turns off the spectrometers and puts the s
43. file HYDRORAD CMD if it exists Also the file TRIGGER cMD if it exists will be executed whenever the trigger switch is engaged Command files can be created and edited using a Windows text editor then downloaded onto the flash card as described in section 6 4 9 1 GENERAL FORMAT Each line has one command followed by a carriage return and optional linefeed Commands have the same format they would have if entered in real time 9 2 SIMPLE EXAMPLE auto 1 20 auto 2 20 auto 3 20 The above example simply determines the optimal integration time for channels 1 2 and 3 Nothing is saved to the flash disk 9 3 TRIGGER CMD EXAMPLE pause 10 logauto 5 samples 1 divel The above example was used for a diver operated HydroRad Whenever the trigger switch is toggled the HydroRad will wait for ten seconds while the diver gets out of the way For each channel 5 spectra will be collected and averaged and the average from each saved in a file with the base name divel The HydroRad will then return to a waiting state If the trigger switch is turned off while the command is still in progress it will be cancelled 49 Note that the operation of the trigger switch has changed as of firmware version 1 31 See section 7 2 for details 9 4 TIMED COMMAND FILE FORMAT Timed commands are preceded by a time in the form HH MM hours and minutes with a comma separating the time from the command Note that whereas command argu
44. for later processing 10 3 CALIBRATION FILES To apply any of the calibration processing steps a calibration file for each active channel of the HydroRad must be stored on the flash disk Calibration data for each instrument and channel are generated during HOBI Labs calibration then transferred to HydroRad in the form of an ASCII comma separated values file This file must be converted by the HydroRad operating software into binary files of the proper format for 54 each channel This conversion is performed by the IMPORTCAL command see 8 2 10 The conversion is only needed once then the csv file can be deleted The working calibration files are named a CAL B CAL etc HOBI Labs normally loads these files at the time of calibration Note that these files are not the same as the cat files that were generated similarly by HRCAL software that is now obsolete 10 4 ASCII CALIBRATION FILE FORMAT The file is split up into sections which can be in any particular order Sections are identified by strings in square brackets e g ID The firmware ignores extra lines outside the defined sections and ignores extra information at the end of lines as long as it is separated by a comma There is one section that identifies the HydroRad and four sections associated with the calibration of each HydroRad channel The equations to which this calibration data applies are Do time invariant Dark Offset Average Signal from Pixels Dojow to
45. ger to the instrument before plugging the charger into an AC outlet While the battery tolerates indefinite periods of charging repeated prolonged charges can eventually degrade battery capacity For best battery life we recommend that you charge on average not more than 3 times the time that the sensor is operated from the battery not including sleep time 5 3 4 Battery Disable The battery can be electronically disconnected from the HydroRad circuitry by shorting pins 2 and 8 of the bulkhead connector together HOBI Labs supplies a special dummy plug distinguished from a standard dummy by a pink or red handle for disconnecting the battery You should apply this plug when shipping or storing the instrument for long periods to protect the batteries against excessive discharge The battery disconnect plug can also be used to reboot the instrument in case of a software fault In some cases it may be desirable to permanently disable the battery if HydroRad is to be externally powered for several months on a mooring This will require a communication cable that shorts pins 2 and 8 This will protect the instrument firmware from hanging if the batteries drain to a very low voltage level due to current leakage and the external voltage is accidentally cycled However the mooring controller will then 17 have to reset the HydroRad s clock In most cases it is preferable to leave the batteries connected so that the HydroRad s cloc
46. ime gt 4 byte integer lt Temp gt 4 byte IEEE floating point lt Voltage gt 4 byte IEEE floating point lt Depth gt 4 byte IEEE floating point lt Process gt 2 byte integer lt N gt 2 byte integer lt Scale gt 4 byte IEEE floating point lt Do gt 4 byte IEEE floating point lt Dt gt 4 byte IEEE floating point lt IntTime gt 4 byte integer lt FirstPix gt 2 byte integer lt PixInc gt 2 byte signed integer lt PixCount gt 2 byte integer lt Pixel FirstPix gt see below lt Pixel First PixInc gt see below lt Pixel FirstPix PixCount 1 PixInc gt lt CRC16 gt 2 byte integer Prompt optional 1 byte 0x3F or Wave0 is the zero order wavelength coefficient times 10 2 6 divide by 640 0 to get coefficient Wavel is the first order wavelength coefficient times 10 216 divide by 655360 0 Wave2 is the second order wavelength coefficient times 10 2426 divide by 671088640 0 If the value of process is zero or one then the pixel values are 2 byte integers If process is greater than one the pixel values are 4 byte IEEE floating point values The most significant byte of each value is stored first opposite to the native byte order on DOS and Windows PCs Prompt is only sent in Prompted CRC mode and only if the data is being sent directly out the serial port If the host replies with a Y or y the HydroRad will continue with other tasks If the host replies with an X or x indicating
47. indicates the number of samples in an averaged sample and has the value 1 if no averaging was done IntTime is the integration time in milliseconds FirstPix PixInc and PixCount indicate the range of pixels included in the saved spectrum 10 7 BINARY CRC amp PROMPTED CRC FILE FORMATS The binary CRC data format was created to allow a real time data collection system to know if the binary data it is receiving is error free by including a binary checksum in the data In prompted CRC mode the real time data collection system can actually request re sends of bad data packets Binary CRC data also includes all the information required for displaying the data at its current level of calibration without requiring an external calibration file The Binary CRC Prompted CRC data sequence is as follows OCCO 2 bytes 0x0C and 0xCO0 lt Model gt 4 ASCII bytes lt Serial gt 12 ASCII bytes lt Channel gt 1 byte Channel A 0 B 1 te lt FiltType gt 1 byte 0 1 or 2 lt FiltSize gt 2 byte signed integer lt CalSource gt 12 ASCII bytes lt ChanName gt 8 ASCII bytes lt ChanUnits gt 12 ASCII bytes lt Wave0 gt 4 byte integer lt Wavel gt 4 byte integer lt Wave2 gt 4 byte integer 59 lt Depthoffset gt 4 byte IEEE floating point lt DepthCoeff gt 4 byte IEEE floating point lt RawT
48. ing solution such as Edmund Lens Cleaner Edmund Optics part number 54828 and a non abrasive tissue then rinse with pure water For stubborn contamination you may use detergent or ethanol Do NOT use acetone which will damage the plastic parts 14 Pressure Transducer The pressure transducer is located under a reservoir of silicone oil which has a cap and a long thin tube sticking out of it The reservoir may need occasional refilling this is normally performed by HOBI Labs during regular maintenance 1 5 Electrical Connectors Occasionally apply silicone lubricant such as Dow Corning DC111 or a silicone spray to the connector pins Do not use any petroleum based lubricant especially WD 40 The connectors should mate smoothly without great force Well lubricated connectors also separate fairly easily so always use the locking sleeves NOTE use care to avoid contaminating the light collectors with lubricant 1 6 Mounting and Deployment For profiling the HydroRad should be secured in a HOBI supplied cage or strapped to another support If using metal straps or clamps to secure it use padding to avoid marring the HydroRad case 1 7 Batteries For HydroRads that contain internal batteries use the red handled battery disconnect plug to avoid over discharging the batteries during shipping and storage Fully charge the batteries at least every two months 1 8 Packing and Shipping Use the shipping container and protective foam
49. k is maintained during mooring power outages Note that like the hard disk in a computer HydroRad s flash disk can be corrupted if power is removed while it is updating its directory Therefore do not disable the battery while HydroRad is storing data or performing file operations If you remove power when the indicator light is green or off there is no risk of losing data Disabling the battery will cause HydroRad s real time clock to reset and will also reset any parameters that were changed without being saved to flash by the SAVEPARAMS command 18 6 COMMUNICATIONS HydroRad communicates through a standard RS 232 serial connection to any computer serial port Any common terminal emulator program can be used but RadSoft is preferred as it has many features tailored specifically for the HydroRad 6 1 COMMUNICATION PARAMETERS HydroRad s serial protocol is 8 bits no parity 1 stop bit and no flow control Only the transmit receive and ground lines are connected between HydroRad and the computer 6 2 BAUD RATES The default communication rate is 9600 baud some systems are shipped however with the baud rate set to 57600 as described in section 6 3 9600 baud is robust and adequate for routine communication with the instrument but when downloading large amounts of data it is desirable to increase the rate by using the BAUD command see 8 2 2 Standard baud rates from 300 to 230 400 baud are supported Note that most
50. mand preceded by a backslash will be passed to PicoDOS for execution In this manner you can execute any PicoDOS command from within HydroRad This is not needed under normal circumstances WARNING Although you can use this mechanism to launch another program or run a PicoDOS batch file from within HydroRad this is not advisable It leads to a disorderly exit from HydroRad and the computer may not return to HydroRad upon completion of the other program 8 3 4 BATT Displays the current supply voltage and charge current if battery is being charged This is typically the voltage of the internal battery but may also be supplied by an external source If the external source s voltage is higher than the battery voltage its voltage will be reported The voltage reported will be somewhat lower than actual voltage of the source since it is measured after passing through a protective diode 8 3 5 DEPTH Displays the current calibrated depth reading in meters 8 3 6 Filename Executes the command file FILENAME CMD if it exists See section 9 for a discussion of command files Synonymous with typing RUNFILE Filename 8 3 7 PAUSE Seconds Used primarily in command files PAUSE illuminates the red indicator waits for the given number of seconds 5 if Seconds is not specified then switches the indicator to green 8 3 8 PICODOS Exits the HydroRad program and sends control to the PicoDOS operating system prompt Note that i
51. measurement of the most common radiometric quantities but users may also connect inputs from other sources 3 3 Control Electronics A miniature computer controls all aspects of HydroRad s operation Its primary functions are to control power to the spectrometers and other subsystems generate timing signals for the spectrometers digitize the spectrometer outputs calibrate and filter data store data in flash memory accept configuration instructions and commands from the user execute commands stored in files sleep and wake according to programmed schedules download data from flash memory The user interacts with the controller by sending commands and receiving replies over an RS 232 serial link A large variety of commands let the user configure and control HydroRad for many different situations HydroRad can also run sequences of commands stored as files in the flash memory in the manner of MS DOS batch files HydroRad command files can include assigned times at which specific commands are to be executed allowing users to set up arbitrary data logging schedules When not actively collecting data the controller can be instructed to go into a low power sleep mode to preserve power in the batteries This combined with scheduled command files allows HydroRad to operate autonomously for extended periods while powered by its internal batteries 3 4 Data Logging and Processing The flash memory in Hydro
52. ments may be separated with a space or comma scheduled commands MUST be separated from their times by a comma only Lines that contain a time but no command instruct HydroRad to repeat the last executed command at the designated time 9 5 EXECUTION When a file is run HydroRad begins by executing commands in the sequence they are found in the file If the file contains no timed commands HydroRad simply executes them once in order then closes the file and returns to interactive mode When HydroRad encounters a scheduled command it goes into low power sleep mode until the scheduled time then wakes and executes the command On its first pass through the file HydroRad will skip any commands whose times have passed HydroRad continues executing commands in sequence unscheduled commands as soon as they are read and scheduled commands according to their designated times When it reaches the end of the file or if all the schedule times have already passed HydroRad will return to the first scheduled command in the file and wait for that time to arrive on the following day If a file contains no timed commands HydroRad will execute all the untimed commands once then return to the HydroRad gt prompt If the file contains one or more timed commands it will repeat the schedule every day until halted by the user 9 6 HALTING EXECUTION To halt execution of a command file press lt control c gt You may need to repeat this several tim
53. n that for each data sample the instrument may take several measurements FIXED re uses the last integration time or the times specified in the TIMES command SPEED default uses auto integration for the first data collection and then makes only one measurement per subsequent data collection Occasionally data samples will be over or underexposed but overall the data sampling rate will be maximized The second parameter Count specifies the number of samples to take If the word SECONDS or an abbreviation as short as sec appears as the next argument then Count is to be interpreted as a duration in seconds during which data should be collected If Average is nonzero only one averaged spectrum will be produced for each active channel Otherwise each spectrum measured will be sent to the host and or saved If BaseName is specified and Dest setting indicates data are to be saved in multiple files the file name for each channel will be formed from the BaseName followed by a letter indicating the channel A 1 B 2 etc followed by an extension indicating the data format If the Dest setting indicates data are to be saved in a single file the letter indicating the channel will be omitted If BaseName is not specified the base name will be the date in the form MMDDYY The Process parameter controls which calibration steps are applied to data before they are filtered and saved 0 raw unprocessed default for Acquire c
54. n the channel This could be used for example to boost the output of a detector that is put behind a neutral density filter Line 4 gives the inclusive range of pixels to be averaged to produce the Time Invariant Dark Factor Do Line 5 gives the inclusive range of pixels to be averaged to produce the Time Variant Dark Factor Dt Line 6 gives the number of the first pixel for which calibration data is supplied Lines 7 and up contain for each pixel the factor F used in FixFunction the constant C used to calculate the DarkCorrection and the values of e epsilon and Immersion used in calculating Engineering Units The firmware will keep reading pixel values from successive lines until it hits a line that doesn t begin with a digit or until the pixel number reaches 2047 Example channel information dark correction epsilon and immersion correction A Edl name of the channel 31 chars max W m 2 nm physical units 31 characters max 1 overall scale factor 3 18 Do Low and Do High 20 35 Dt Low and Dt High 1 number of first pixel for which calibration data is provided 3 0 01319 0 2019938 1 3991 F 1 C 1 epsilon 1 Immersion 1 1 0 01351 0 2019345 1 3991 F 2 C 2 epsilon 1 Immersion 2 1 0 00243 0 2018741 1 3992 etc 4 0 00862 0 2018413 1 3992 56 10 4 3 Non Linearity The values in this table are used in the lineari
55. name of the channel and the units of calibrated data produced by the channel The name and units may not be included if raw data are recorded In ASCII files each spectrum is saved as a line of comma separated decimal values as follows RawTime Temp Voltage Depth Process N Scale Do Dt IntTime FirstPix PixInc PixCount Pixel FirstPix Pixel FirstPix PixInc Pixel FirstPix PixCount 1 PixInc lt return gt lt linefeed gt RawTime is the time of the sample in seconds since 00 00 on Jan 1 1970 If using Excel to display data you can use the following formula to convert the time to a conventional date time format rawTime 86400 DATEVALUE 1 1 70 58 Temp Voltage and Depth are real numbers representing the internal temperature in C the supply voltage in volts and the depth in meters Process indicates what steps in the calibration process have been applied to the data A value of zero indicates the data are raw 4 indicates they are fully calibrated and in engineering units Intermediate values indicate intermediate steps in the process Scale is a number by which all the pixel values must be multiplied to restore them to their correct values As of firmware version 1 00 this number is always set to 1 0 Do and Dt are used in the dark current calculation portion of the calibration procedure They are needed to calibrate raw data or to convert calibrated data back to raw N
56. nd the battery charging current The battery voltage gives a rough indication of how much charge remains When the battery voltage falls below 11 V indicating it is virtually completely discharged the HydroRad should not be used in battery mode 16 operation HydroRad will go into its low power sleep mode whenever the voltage falls below this threshold 5 3 3 Charging HydroRads with batteries installed include constant current chargers that recharge the battery in a maximum of 15 hours Any replacement charger used for a HydroRad should put out between 18 and 27 volts DC chargers that put out less than 18 volts will not be able to fully charge the HydroRad The actual charging time required after a partial discharge is about 40 longer than the full power operating time for a HR 4 and about equal to the full power operating time for a HR 2 Charging continues at the same rate as long as the charger is plugged in If the HydroRad is operating with the battery charger plugged in note that the current going to the batteries will be reduced and the charging time will increase For a HR 3 or HR 4 continuously sampling the batteries can drain even with the charger plugged in For fastest charging either put HydroRad to sleep or provide an external power supply whose voltage is higher than the battery voltage A 13 8V power supply is recommended for this situation NOTE to protect against disruptive transients connect the output of the char
57. nd the currently loaded filter coefficients if any 8 2 9 ID Displays the factory set model serial number and configuration information about the HydroRad 8 2 10 IMPORTCAL Filename Given a file containing properly formatted calibration data for one or more channels translates the file into a binary format for future rapid loading The resulting binary files are named a cat for channel 1 8 CAL etc If the DAISYCHAIN command is used IMPORTCAL does NOT have to be repeated 8 2 11 INTPARAMS MinTime MaxTime WarmupTime AutoPowerDown Channels Shows and sets parameters governing integration MinTime is the minimum integration time in milliseconds used in auto integration commands such as AUTO LOGAUTO and START This is typically set to the electronic limit of 20 ms MaxTime is the maximum integration time in milliseconds used in auto integration commands such as AUTO LOGAUTO and START Practical values of MaxTime range from 2000 to 30000 milliseconds although it can be set higher WarmupTime is the number of seconds HydroRad will wait before collecting spectra after power is first applied to the spectrometers AutoPowerDown can be either zero or a number greater than zero If it is nonzero then power to the spectrometers will be turned off if they are idle for more than 2 seconds plus WarmupTime Channels is a string of digits or letters specifying from which channels data will be collected For example 13 or AC indi
58. nds then the data is re sent up to 10 times per channel 1 spectra saved in binary with CRC checksum BIN extension on files 0 spectra saved in binary BIN extension on files 1 spectra saved in text ASC extension on files The Dest parameter selects where data are output the default setting is to use the LogParams OutputDestination setting 0 multiple files Channel letter appended to file name 1 single file host console default for Acquire command 2 3 host console multiple files 4 host console single files 40 Channels is a string of digits indicating with spectrometer channels are enabled For example 124 indicates that channels 1 2 and 4 are enabled By default the channels specified in the IntParams Channels setting are used FirstPix LastPix and PixInc are used to sub sample the measured data They determine which pixels will be included in the output spectrum If Pix nc is a positive number then FirstPix LastPix and PixIncrement will correspond to physical pixels If PixInc is a negative number and a calibration has been imported into the HydroRad see ImportCal then FirstPix and LastPix and PixInc will be 10ths of nanometers For example if 400 2000 and 2 are specified then the output will consist of pixels 400 402 404 406 2000 If 3500 8500 and 25 are specified then output will consist of pixels corresponding to wavelengths at 350nm 352 5nm 355nm 357 5nm 850nm
59. ne at any time to change the default rate If you want the new AUTOEXEC BAT or lack of one to take effect immediately type RESET lt enter gt at the HydroRad prompt 6 4 File Transfers using the RadSoft Device Explorer From the RadSoft Desktop if there is more than one device click on that device to select it and Select Device Explorer 2 from the File menu there is only one device then it will be automatically selected After a pause during which lines will scroll in the Terminal window a window like the following will appear Fahr990501 Explorer Op x File Edit View Window Pmi Blo x lle ne OT SIE iit CAL File 05 20 03 16 35 20802 CAL File 05 20 03 16 37 27 CAL File 06 27 03 16 55 406570 CSX File 05 20 03 16 33 91121 HydroRad Binary Files 06 19 03 12 14 91121 HydroRad Binary Files 06 19 03 12 14 29498 HydroRad Binary Files 06 27 03 16 27 29498 HydroRad Binary Files 06 27 03 16 2 4181 HvdroRad Binary Files 06 04 23 11 5 zi 47 280 128 bytes free sl CALCKO1B BIN 40 fles After the directory is loaded select the data sets or casts you wish to retrieve Right click on the selected files to bring up a menu which will allow you to either get the files from the instrument and save them to disk or to open them directly in RadSoft If you choose to get the files from the instrument then you will be prompted for a directory into which
60. o 3 and the day to 1 without affecting the year and times for example 13 24 sets the hour and minute without affecting the seconds Years may be entered with 2 or 4 digits 8 2 7 ECHO state or ECHO string State specifies whether characters sent to HydroRad s serial port are automatically echoed If state is on 1 then echo is turned on if state is off zero then echo is turned off The default is on With echo off characters you type will not appear in your terminal software If a string follows the echo command the string will be echoed to the command line Be careful because if the first word of the string is one of the HydroRad reserved 66 words on open yes off close no the value of the reserved word will be used as if you were specifying a State and the rest of the string will be ignored 8 2 8 FILTPARAMS FirstPixel LastPixel Pixellncrement FilterSpec FilterSize Before a spectrum is saved by one of the logging commands LOG LOGFIXED LOGRANGE LOGAUTO or displayed by the FILT command it is filtered by convolution with a filter specified by the parameter FilterSpec Then a subset of pixels defined by the FirstPixel LastPixel and Pixellncrement parameters is selected from the filtered spectrum IMPORTANT If you set Pixellncrement to a value other than 1 you should set the processing parameter of LOGPARAMS to a value of 1 or higher See section 10 2 for information ab
61. ommand 1 weak pixel adjustments 2 dark current compensation 3 normalized by integration time 4 engineering unit scaling full calibration The Format parameter selects the format in which data are output 36 2 spectra saved in binary with CRC checksum and host reply BIN extension on files If the output is to the console the data is followed by a Within 2 seconds the host must respond with an acknowledgment of good data Y or an indicator of bad data X If bad data is indicated or no response is received in 2 seconds then the data is re sent up to 10 times per channel default for Acquire command 1 spectra saved in binary with CRC checksum BIN extension on files 0 spectra saved in binary BIN extension on files 1 spectra saved in text ASC extension on files The Dest parameter selects where data are output 0 multiple files Channel letter appended to file name 1 single file 2 host console default for Acquire command 3 host console multiple files 4 host console single files Channels is a string of digits indicating with spectrometer channels are enabled For example 124 indicates that channels 1 2 and 4 are enabled By default all channels are enabled for the Acquire command FirstPix LastPix and PixInc are used to sub sample the measured data They determine which pixels will be included in the output spectrum If Pix nc is a positive number then FirstPix LastPix an
62. originally supplied with your HydroRad and follow any packing instructions included with it Be especially careful that the fiber optic cables are not coiled tightly and cannot be pinched by the instrument or case 2 1 Sleep Wake shown 2 QUICK START Fiber optic penetrators light collectors configuration varies 2 pin Shutter Connector optional in sleep position Indicator Pressure Relief Valve Daisy chain connector optional Pressure sensor port optional Power Data Connector Basic Hookup Requirements Windows computer with an available serial COM port may be a USB serial converter Installation program for RadSoft either from a CD supplied with your instrument or downloaded from www hobilabs com Calibration file for your HydroRad also on a CD supplied with your instrument This is not strictly required but is much faster than downloading the file from the instrument HOBI supplied Power data interface PDI cable or equivalent HOBI supplied battery charger Procedure 1 Install RadSoft on your computer 2 Connect the PDI cable to a serial port on your computer 3 Connect the PDI cable to the 8 pin power and communications connector on the HydroRad 4 5 6 7 8 9 Plug the cord from the battery charger transformer into the barrel connector on the data cable Plug the battery charger into a 120 VAC jack Start RadSoft
63. ount Alternatively the word SECONDS or an abbreviation as short as sec may appear as the second argument indicating that the first is to be interpreted as a duration in seconds during which data should be collected Examples LOGAUTO 3 hydro 41 For each channel 3 spectra will be collected and averaged and the average from each saved in a file with the base name hydro LOGAUTO 30 sec 1 hydro For each channel spectra will be collected and averaged and the average from each saved in a file with the base name hydro for a total of 30 seconds The exposure time for each channel is set automatically to maximize the dynamic range within the limits set with INTPARAMS After the optimum integration time is determined each spectrum is filtered according to the current FILTPARAMS then saved in a file or transmitted to the serial port depending on the OutputDestination set in LOGPARAMS If Average is nonzero only one averaged spectrum will be produced for each active channel Otherwise each spectrum measured will be saved If BaseName is specified and the OutputFormat setting in LOGPARAMS indicates data are to be saved in a file the file name for each channel will be formed from the BaseName followed by a letter indicating the channel A 1 B 2 etc followed by an extension indicating the data format see LOGPARAMS If BaseName is not specified the base name will be the date in the form MMDDYY If a value is s
64. out how filtering and selecting pixels can affect the quality of your data If PixIncrement is a positive number then FirstPix LastPix and PixIncrement will correspond to physical pixels If PixIncrement is a negative number and a calibration has been imported into the HydroRad see ImportCal then FirstPix and LastPix and PixIncrement will be 10ths of nanometers New in firmware version 1 29 FilterSpec can be 0 1 or 2 A value of 0 zero or off specifies no filtering A value of 1 specifies boxcar averaging in which case each pixel in the output spectrum will be the result of an equally weighted average of the number of pixels or wavelength range specified by FilterSize rounded up to an odd integer if necessary A value of 2 specifies Gaussian averaging where each pixel in the output spectrum will be the result of an normal distribution weighted average with a full width at half max FWHM equal to the number of pixels or wavelength range specified by FilterSize 29 Prior to firmware version 1 29 FilterSpec could be a file name This is no longer supported If FilterSize is a positive integer then it will correspond to that fixed number of pixels If FilterSize is a negative integer then the filter width will be that many 10ths of nm wide So a FilterSize of 5 specifies a 5 pixel wide filter A filter size of 15 specifies a 1 5 nm wide filter Whether or not arguments are specified FILTPARAMS displays the parameters a
65. pecified for Process this value will override the Processing value set up with the LogParams command This parameter controls which calibration steps are applied to data before they are filtered and saved 0 raw unprocessed 1 weak pixel adjustments 2 dark current compensation 3 normalized by integration time 4 engineering unit scaling full calibration Note that when Seconds is specified Count is actually a minimum LOGAUTO only checks each time it finishes the last channel to see whether it has exceeded the specified time In the worst case it could finish one cycle shortly before the time limit then do another measurement on all channels before stopping So the actual time could be as much as the maximum integration time multiplied by the number of channels greater than Count To force LOGAUTO to cycle through the channels only once set Count to 1 without the seconds option A pair of control c characters received through the serial port during execution of LOGAUTO will abort the process 42 8 4 10 LOGFIXED IntTime Averages BaseName Process The LogFixed command has been deprecated see Acquire and Log Commands LOGFIXED integrates each channel for the same fixed integration time given in milliseconds by ntTime However if IntTime is not specified each channel will integrate for the time of its last integration In this case the integration times may be different from channel to channel The ntTime parame
66. r size of 15 specifies a 1 5 nm wide filter By default FilterSize is 0 no filtering 8 4 2 AUTO Channel IntTime Collects a spectrum to memory from the given channel automatically seeking the optimum integration time If ntTime is specified it will try that time first If not it will start with the integration time that was last used for that channel regardless of which command triggered the previous integration If no Channel is specified it will collect from the last used channel Channel may be entered as a letter a number or an asterisk to indicate all channels 8 4 3 AUX Collects and shows one sample of data from the NMEA output auxiliary device if one is attached 8 4 4 CHAN Channel If no Channel is specified displays the most recently used spectrometer channel If a Channel is specified sets the current channel to that value Channel may be entered as a letter a number or an asterisk to indicate all channels This channel setting will be used as the default channel for subsequent AUTO or INT commands 8 4 5 FILT FirstPixel LastPixel Pixellncrement Channel Displays the most recent spectrum collected with INT or AUTO after applying the current filter see FILTPARAMS If Channel is specified or an asterisk for all channels the most recent spectrum from that channel is shown Press Control C or send an ASCII code 03 to break out of the listing 8 4 6 GRAPH FirstPixel LastPixel VerticalScale Ch
67. roRad configuration includes internal rechargeable batteries Note however that in cases where the instrument will operate for long periods more than a few weeks without charging the batteries it is preferable to disable them or leave them out entirely For this reason some HydroRads may not contain batteries 5 3 1 Battery Capacity The capacity of the battery depends on the temperature at which it is charged stored and discharged Charging and storage at temperatures of 20 C or less improve capacity On the other hand low temperatures during discharge lower the realized capacity Peak capacity for a battery charged and discharged at room temperature is 12 hours of continuous operation with an HR 2 and 8 hours with a HR 4 In response to the sleep wake switch being turned to sleep or the SLEEP software command the HydroRad will enter a low power sleep state during which its current drain is reduced to about 1 mA In this state fully charged batteries will last about 2 months Hourly sampling schemes can typically last about 1 month Capacity decreases slowly as the battery ages The capacity loss depends greatly on charging conditions but is typically less than 10 after 200 charge discharge cycles and 20 after 500 cycles 5 3 2 Battery Voltage and State of Charge To read current value of the battery voltage whenever communication is established with the sensor enter the BATT command This will display the current voltage a
68. s the sensor from sleep Because the switch only signals the sensor to sleep or wake it is possible to wake HydroRad with serial communication from a computer even if the power switch is in the off position It is likewise possible to command the sensor to sleep even if the switch is on Switching the power switch to off while the sensor is asleep will have no effect Note that the sleep and wake functions only work while the HydroRad operating program is running and will not work when running PicoDOS 7 2 TRIGGER SWITCH PLEASE NOTE OPERATION OF THE TRIGGER SWITCH WAS SIGNIFICANTLY DIFFERENT IN FIRMWARE VERSIONS PRIOR TO 1 27 The second switch triggers data collection If the sensor is awake the trigger switch signals the HydroRad firmware to execute a command file TRIGGER cMD This allows the user to specify an arbitrary response to the trigger switch If no TRIGGER CMD file is present on the flash card the START command will be executed which periodically runs the LOG command with the default parameters set in the LOGPARAMS command If a TRIGGER CMD is present it will be executed once To cause a command in the trigger cmd file to be repeated use the syntax START Command within the trigger cmd file If several commands must be repeated use the syntax START repeat cmd where repeat cmd is a second command file containing the commands to be repeated Switching off the trigger switch cancels any running commands or d
69. sscssssccssscscccsssccessscsesscsesccssssccesssssessssssscseess 16 5 35 Internal Battery esse wese sesse ge eg gee Ged ee EG eed bo ke gs ee ek oe We bog gee 16 6 COMMUNICATIONS oes bees iese see bees se Sies bes see wee ie de ee Geek ese Fe ek Se ee Se Gede 19 6 1 COMMUNICATION PARAMETERS sesse esssssss sees ee sees se se ee ee de ee ee Ge Ge ee ee Ge Ge ee ee 19 62 BAUD RATES eise siste ss ss segoed ee ese oe se bees eo de ee ed eo od ob oog ee be eg ee esia GR GE 19 6 3 CHANGING DEFAULT BAUD RATE sees ee sesse sees ee sees es ss se see ee ese ee se se ee ee de ee Ge Ge ee ee ee 19 6 4 File Transfers using the RadSoft Device Explorer sesse sesse esse esse ee ees Ee BEG Ge se Gee 20 Te EXTERNAL SWITCHES is se ees ole esse gesek se bes Seg oek De ee De ey gee ee Vee e see Ges ek See ese 23 Fels SLEEP WAKE S WITCH icc eis sissies sees see see ede eo sd sees dee ese sd ee bee ee ee dee ee see ese se de eed ee 23 72 TRIGGER SWITCH iese sees ee oes se dose ed ees de be dood Gee dee dd Ed be de seg ed dd oe si de ek eed de de eed 23 iii COMMANDS EE ee a ee ee rE OTN 25 8 1 COMMAND CONVENTIONS ueesee se esse ese sees se ee Ee SEE Be Ee SEE EE ee EE RE Be EE SEE Be Be ee Ee 25 8 2 CONFIGURATION COMMANDS ee esee see sees se ese see See Ee SEE SEE Se EE RE Be Ee Ee EE Ge Ee Se ee ee 26 8 3 GENERAL OPERATIONS ese ssee see ese ese esse sees se ese See Be ee ee SEE Dee Ee GEE SEE Re Se EE SEE Be Ee ees 33 84 DATA COLLECTIO
70. t 1 PixInc gt If the value of process is zero or one then the pixel values are 2 byte integers If process is greater than one the pixel values are 4 byte IEEE floating point values The most significant byte of each value is stored first opposite to the native byte order on DOS and Windows PCs 10 9 DATA FILE SIZES File sizes vary widely according to their format and the number of pixels included They can be reduced drastically to as little as a hundred bytes by setting the FILTPARAMS to select a small subset of pixels although subsampling requires careful attention to the appropriate processing level see 10 2 A good compromise between file size and data security is to save all the raw pixel data in binary form Saving all 2048 pixels results in spectra of about 4200 bytes In most cases the number of spectrally useful pixels is closer to 1500 reducing the spectra to about 3200 bytes With the minimum 4 Mbyte flash card this gives a practical capacity of over 1000 spectra 61 Whereas raw binary files save pixels as 2 byte integers processed pixels are stored as floating point numbers requiring twice the space ASCII files are the easiest to read but can be as much as five times larger than raw binary files and two to three times larger than processed binary files up to 20 000 bytes per spectrum For many applications even this size is not prohibitive but clearly the user must consider data capacity for long term or
71. tant fraction of the saturation response across the spectrum The curves differ from each other by a factor of about 2 000 000 which is the total system dynamic range for a given wavelength Within a single spectrum with 10nm bandwidth averaging the S N is typically 1000 1 for a full scale signal and the raw dynamic range ratio of full scale reading to RMS dark noise is greater than 2000 1 The dynamic range is higher than the S N because the absolute noise actually decreases at lower signals The noise level can be decreased further with additional bandwidth averaging averaging of multiple spectra or both Saturation Irradiance 21 ms integration time 2 Irradiance W cm nm Dark noise in 10 nm BW 10 Hi 20s io time 350 400 450 500 550 600 650 700 750 800 850nm Wavelength nm Saturation radiances and effective dark noise irradiance of standard configuration set for maximum sensitivity 13 5 POWER AND DATA CONNECTIONS HydroRad can be powered from three sources 1 External 10V to 15V supply 2 Internal battery 3 External 18V to 24V battery charger Any combination of these sources may be safely connected simultaneously NOTE voltages above 15V can only safely be applied to the battery charging input Power will be drawn from the source with the highest voltage Nominal power draw at 12V input is 50 mA plus 70 mA per channel during sampling and 1 mA during low power sleep
72. ted If Average is nonzero only one averaged spectrum will be produced for each active channel Otherwise each spectrum measured will be sent to the host and or saved 39 If BaseName is specified and the Dest setting indicates data are to be saved in multiple files the file name for each channel will be formed from the BaseName followed by a letter indicating the channel A 1 B 2 etc followed by an extension indicating the data format If the Dest setting indicates data are to be saved in a single file the letter indicating the channel will be omitted If BaseName is not specified the base name will be the date in the form MMDDYY The Process parameter controls which calibration steps are applied to data before they are filtered and saved the default setting is to use the LogParams Processing setting 0 raw unprocessed 1 weak pixel adjustments 2 dark current compensation 3 normalized by integration time 4 engineering unit scaling full calibration The Format parameter selects the format in which data are output the default setting is to use the LogParams OutputFormat setting 2 spectra saved in binary with CRC checksum and host reply BIN extension on files If the output is to the console the data is followed by a Within 2 seconds the host must respond with an acknowledgment of good data Y or an indicator of bad data X If bad data is indicated or no response is received in 2 seco
73. ter may also take the form of ntTime IntTime IntTime or IntTime In this case the operator specified and the new ntTime argument will be applied to the previous integration time for the channel So if the previous integration time for channels A and B were 135 and 178 ms respectively and the command LOGFIXED 3 was used channels A and B would be integrated for 405 and 534 milliseconds respectively This may be useful for intentionally overexposing the spectrometer after a LOGAUTO command to get better resolution in the UV in UR ranges at the expense of over saturation in the midrange If Averages is specified and greater than 1 that number of integrations will be performed and each channel s average spectrum saved IMPORTANT See section 10 2 for information about how averaging can affect the quality of your data If the OutputFormat parameter of LOGPARAMS specifies data are to be saved in files the files one for each channel will be named with BaseName followed by a letter A through D designating channel 1 through 4 followed by the extension DAT If BaseName is not specified the base name will be formed from the current date in the form YYMMDD If a value is specified for Process this value will override the Processing value set up with the LogParams command This parameter controls which calibration steps are applied to data before they are filtered and saved 0 raw unprocessed 1 weak pixel adjustments 2 d
74. the LOGPARAMS command When sampleDuration samples have been collected the HydroRad will go into low power sleep mode until SampleCycle seconds have passed since the beginning of the previous collection This is equivalent to switching the Trigger switch to ON Control C or switching the Trigger switch to OFF stops automatic sampling 8 4 15 STOP Halts data collection initiated by START 8 5 FILE OPERATIONS 8 5 1 CAPTURE Filename Opens the file named Filename and copies lines of text to the file as they are typed Editing keys may be used to edit each line as it is typed During editing the prompt changes to Capture gt The file is closed when a lt control z gt character is received CAPTURE automatically overwrites any previously existing file called Filename The RadSoft Terminal cut and paste functions on the Edit menu may be used to give this command considerable power 8 5 2 COPY File1 File2 Copies the contents of File to File2 8 5 3 COPY CON FileName or COPY CON FileName Synonymous with CAPTURE FileName 45 8 5 4 DEL Filespec Deletes the indicated file or files from the flash disk Any combination of and wild cards that can be used with MS DOS can be used with this command The wildcard matches any single character and matches any group of characters For example DEL TEST deletes any file whose name starts with TEST followed by any single character and with any extension TESTA DAT
75. to save the files You may also simply drag the selected files from the RadSoft Explorer into a Microsoft Windows folder or onto the Windows Desktop Depending on the quantity of data and baud rate downloading may take some time Status messages and a graphical indicator will show the download progress You can select arbitrary groups of data sets for downloading To select a contiguous group of casts click on the first item in the group then shift click on the last 20 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 Text files can also be sent to the HydroRad though the device explorer Either drag the text files into the device explorer window or select Send File To Instrument from the Device Explorer s File menu 21 7 EXTERNAL SWITCHES HydroRads include magnetically coupled switches that can be used to control the sensor without connecting to a computer See the figures below for the location of these switches 7 1 SLEEP WAKE SWITCH One switch acts as an on off power switch although it cannot actually turn off power to the sensor When switched from wake to sleep it signals HydroRad to go into an indefinite sleep as if it had received the SLEEP command When switched from sleep to wake it wake
76. ts PreFilter QuickAuto AUTOPARAMNS J J J J J AUTOPARAMS SatValue MinPeak MaxSatPixels MinPeakPixels MaxAttempts PreFilter QuickAuta Shows and sets parameters governing the automatic setting of integration time used by AUTO and LOGAUTO The first four parameters define what is considered an acceptable dynamic range for the pixel values in a spectrum SatValue defines the value at which a pixel is considered saturated MinPeak is the minimum value at which a pixel is considered fully exposed The algorithm will attempt to find an integration time that results in a spectrum that has atleast MinPeakPixels whose values are between SatValue and MinPeak It will allow up to MaxSatPixels that exceed SatValue MinPeakPixels has the lowest priority of the criteria A spectrum may be considered well exposed even if it does not meet MinPeakPixels MaxAttempts is the maximum number of trial integrations allowed The algorithm will terminate after this many integrations if it does not achieve a spectrum that meets the dynamic range criteria Within LOGAUTO the last integration will be logged whether or not it terminated normally PreFilter turns on or off a filter that excludes occasional hot pixels from consideration Under mast circumstances this should be setto 1 QuickAuto determines how multiple channel HydroRads control interleaved auto integration If QuickAuto is enabled non zero or on then channels that have optimum exposure use that d
77. ty correction function Adjustment Corrected Pixel To speed up calculation time and reduce required memory values are interpolated from a lookup table The first two entries 63 and 128 in the example below define the X axis of the lookup table The rest of the data define the Y axis of the lookup table The first Adjustment 1 is at counts 63 the second 4 is at Counts 191 63 128 The third 6 will be at Counts 319 634256 and so on Example non linearity calibration for channel A A NLTABLE 63 128 1 lookup value increment 1 Adjustment factor at Counts 63 4 Adjustment factor at Counts 191 6 Etc 7 T 10 4 4 Time Offset This single value in this section is the amount of time in milliseconds added to the integration time reguested by the HydroRad firmware to account for signal processing delays in the HydroRad hardware Example time offset for channel A A TIME 9 Time Offset 10 4 5 Wavelength Calibration This section contains the three constants Wo Wi and W gt that are used in the second order equation relating pixel numbers to wavelength in nanometers In the example below A WAVE indicates channel A B WAVE would have indicated channel B and so on The text WO W1 and W2 is optional and could have been omitted Example wavelength calibration for channel A A WAVE 32518355 WO 0 38022 Wl 2 192E 05 W2 57 10 5 DAT
78. ystem in low power sleep for the given number of seconds If Seconds is not specified sleeps indefinitely Sleep can always be interrupted by receipt of characters on the serial port or by the sleep wake switch 8 3 15 TEMP Displays the internal temperature of the spectrometers in degrees C 8 3 16 TIMES TimeA TimeB TimeC TimeD TimeE TimeF TimeG Displays the most recently used integration time for each channel If times are specified they will be stored as if they were the most recently used integration time Up to the total number of master amp slave channels may be specified 8 3 17 TOM8 Exits the HydroRad program sets the baud rate to 9600 and enters the TOM8 monitor program Unlike exiting to PicoDOS with the PicoDOS or QUIT command this allows exiting the HydroRad program without executing an AUTOEXEC BAT file if one is on the flash disk Therefore TOMS is not affected by any BAUD instructions 35 8 4 DATA COLLECTION 8 4 1 ACQUIRE AUTO FIXED Count SEC Average BaseName Process Format Dest Channels FirstPix LastPix Pixlinc FilterType FilterSize Collects data from all channels sending the data to the host console by default This command is very similar to the LOG command but uses different default settings The first optional parameter sets the exposure time mode AUTO iteratively tries to find the optimum exposure time for each channel within the limits set with INTPARAMS which may mea
79. zed by integration time 4 engineering unit scaling full calibration A pair of control c characters received through the serial port during execution of LOGRANGE will abort the process 8 4 12 RAW FirstPixel LastPixel Pixellncrement Channel Displays the most recent spectrum collected with INT or AUTO Does not apply the filter but does apply the pixel limits set with FILTPARAMS If FirstPixel LastPixel or PixelIncrement are specified then these values are used in place of the FILTPARAMS limits If Channel is specified or an asterisk for all channels the most recent spectrum from that channel is shown Press Control C or send an ASCII code 03 to break out of the listing 8 4 13 SHUTTER State Delay Opens Shutter open or closes shutter close the detector shutters if attached State can be either open 1 or close 0 Delay determines how long in milliseconds the HydroRad will give the shutters to open or close 8 4 14 START Command If Command is specified it is executed every SampleCycle seconds as specified in the LOGPARAMS command Control C or switching the Trigger switch to OFF stops the loop Command may also be the name of a command file which would be executed every SampleCycle seconds A STOP command in the command file will also break the loop If no command is specified the LOG command executes every SampleCycle seconds collecting SampleDuration samples each time as specified in

HydroRad User`s Manual - Hobi Instrument Services

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