Cycle Host
User's Guide
This guide is an evolving document. If you find sections that are unclear, or missing information, please let us know ([email protected]). Please check our website (www.wetlabs.com) periodically for updates.
WET Labs, Inc. PO Box 518 Philomath, OR 97370 541-929-5650 fax: 541-929-5277 www.wetlabs.com
28 January 2010 Cycle Host User's Guide Revision 1.04 1/59 Cycle Host Installation The following sub-sections detail the steps necessary to install and run the Cycle Host program (also referred to as "the host") for the first time on a new computer. System Requirements Below are the recommended minimum requirements for a computer to be used to run the host program. Although Windows is currently the only supported operating system, future releases are planned to support Linux and MAC OS as well. Please let us know of your interest in these platforms via [email protected].
Feature Requirements Operating System Windows XP/Vista/2000/2003 (32 and 64 bit versions) Memory 128 Megabytes Disk Space 125 Megabytes (excludes data file storage) Data Port Serial port or USB to Serial adapter supporting 19200 baud Input Devices Keyboard (minimum) Mouse or other pointing device (recommended) Monitor Color, 1024 x 768 (minimum recommended) Table 1: Host Computer System Requirements The Java Runtime Environment The Cycle Host program is written in the JavaTM language developed by Sun Microsystems Inc. For this reason, execution of the host requires the installation of the Java Runtime Environment, or JRE. At the time of this release the current JRE is Version 6 Update 16. The host should run with any of the version 6 JREs, but it is recommended that the current version be used.
28 January 2010 Cycle Host User's Guide Revision 1.04 2/59 Figure 1: Java About Window
Verifying the JRE version To verify the currently installed version of the JRE, select the Java icon in the Windows TM Control Panel. Then select the About... button on the General tab. You should see a window similar to Figure 1. If there is no Java icon visible within the Control Panel options, it is likely that there is no JRE installed. Another method for verifying the existence and version of the JRE is to visit the URL www.java.com within a web browser and look for the link "Do I have Java?". Browsing to that link should inform you which version of the JRE is currently installed.
Installing the JRE If your host computer is not connected to the internet, the executable installation file for Windows XP/Vista/2000/2003/2008 is available in the JREDistribution directory on the distribution CD included with the instrument. If your host computer is connected to the Internet, it is recommended that you visit the URL www.java.com and follow the links, on screen prompts and directions provided there to install the most current JRE.
NOTICE: If you are installing the JRE on a computer with the Windows Vista operating system, be sure to follow the steps detailed in the Note To Windows Vista Users section once you have installed the JRE.
28 January 2010 Cycle Host User's Guide Revision 1.04 3/59 Figure 2: Java Update Window
Updating the JRE
Figure 3: Up To Date JRE Message To verify the currently installed version of the JRE, select the Java icon in the Windows TM Control Panel. Then select the Update tab. You should see a window similar to Figure 2. Selecting the Update Now button will perform an immediate check to ensure that the JRE is up to date. It is recommended that automatic updates be enabled to detect future releases as they become available. If your JRE is up to date, you will see a pop-up window similar to Figure 3. If your JRE is not current, a pop-up window similar to Figure 4 will appear.
28 January 2010 Cycle Host User's Guide Revision 1.04 4/59 Figure 4: Java Update Available
Figure 5: Java Setup Welcome
Select the Install button and a new window similar to Figure 5 will appear.
28 January 2010 Cycle Host User's Guide Revision 1.04 5/59 You may choose to view the license agreement if you wish, but the Accept button must be selected for the JRE to be installed. It is highly recommended that the Change destination folder check box (shown highlighted in red) remain deselected.
Figure 6: Yahoo Toolbar Option You may see a pop-up window similar to Figure 6. You may chose to install the Yahoo Toolbar at your discretion. It is not required for the Cycle Host installation. Click the Next button when you have made your selection. After the Next button has been selected, the JRE installation will begin. You will see a progress window similar to Figure 7 during the installation process.
28 January 2010 Cycle Host User's Guide Revision 1.04 6/59 Figure 7: Java Setup In Progress
Once the JRE update is complete, you should see a window similar to Figure 8. Click the Finish button to complete the update.
28 January 2010 Cycle Host User's Guide Revision 1.04 7/59 Figure 8: JRE Update Complete Note To Windows Vista Users The host program will automatically copy several required files into the JRE directories. For this operation to succeed on Vista machines, write access permissions need to be enabled for JRE directory and its subdirectories for any user who will be running the host program. To also ensure access to future JRE installations, it is recommended that the write permissions be set for the c:\program files\Java directory and all of its subdirectories. To change the folder permissions, follow the steps below: 1. Run the Windows Explorer program, browse to the c:\program files\Java directory. 2. Right click on the c:\program files\Java directory and select the Properties option from the pop-up menu. 3. Click on the Security tab from the window that appears. 4. Click the Advanced button. 5. In the Advanced Security Settings window that pops up, click on the Owner tab. 6. Click the Edit button on the Owner tab. 7. Click the Other users or groups button on the new Advanced Security Settings
28 January 2010 Cycle Host User's Guide Revision 1.04 8/59 window that pops up. 8. Click the Advanced button in the lower left corner of the Select User or Group window that pops up. 9. Click the Find Now button from the new Select User or Group window that pops up. 10.Scroll through the Search Results list at the bottom of the window for your current user account and double-click on it. The window will disappear, returning you to the previous Select User or Group window. 11. Your user account should now appear in the text box under Enter the object name to select ( examples ):. Click the OK button on the Select User or Group window. 12.Click the OK button on the Advanced Security Settings for Java window. A Windows Security pop-up window will issue a message about ownership of the object. Click on its OK button. 13.Click the OK button on the next Advanced Security Settings for Java window. 14.When the Java Properties window reappears, select your user account from the list up top and click Edit. 15.Select your user account from the list beneath Group or user names: and then click the Edit button. 16.A new Permissions for Java window will appear. Select your user account from the list beneath Group or user names: again. In the lowest pane labeled Permissions for your user in the, click the box to the right of Full control in the Allow column. It should now have a check mark in the box. 17.Click the OK button. You may see a pop-up window that shows Setting security information on: file names while the files are updated. 18.If You get a security warning, click Yes. 19.Finally, click the OK button on the remaining Permissions for Java window. Installing Cycle Host All the necessary files for the host are in the CycleHost.zip file included on the distribution CD or available at the WET Labs web site. The recommended directory structure (C:\program files\WETLabs\CycleHost) is included within the zip file structure, so simply extract the zip file into the c:\ directory. Any decompression utility that supports the zip file format will be adequate. If upgrading, you may be queried to replace existing files. Click Yes or Yes to All. Starting Cycle Host For most systems, simply navigate to the installation directory (c:\program
28 January 2010 Cycle Host User's Guide Revision 1.04 9/59 files\WETLabs\CycleHost) using the Windows file explorer (Start | All Programs|Accessories| Windows Explorer). Double clicking on the main program file, SAFCycleHost.jar will start the program. The initial splash screen should appear soon thereafter. If it does not, an alternate method is to use the supplied CycleHost.bat batch file in the same directory. The CycleHost.bat file is named CycleHostdotbat within the ZIP file. It must be renamed to CycleHost.bat before it can be used to launch the host program. The batch file will only also work without modification as long as it remains in the same directory as the SAFCycleHost.jar file. Creating Shortcuts
Figure 9: Shortcut Option
In addition to running the host from the installation directory, shortcuts can be created by right clicking on the SAFCycleHost.jar file, dragging it to the desired location (directory, desktop or taskbar) releasing the right mouse button, and selecting the "Create Shortcuts Here" option (see Figure 9). A shortcut created in this manner can then be used to start the host, eliminating the need to use the Windows Explorer application. The same procedure of creating a shortcut can be used to create a shortcut to CycleHost.bat (once it has been renamed as detailed in Starting Cycle Host). Command Line Startup The host can be run from the command line using the following: C:\WINDOWS\system32\javaw.exe -jar "c:\program files\WETLabs\CycleHost\SAFCycleHost.jar" On Windows computers, the JRE installer and Java Updater automatically update the java executable in the \WINDOWS\system32 directory to the current release. Using this location for javaw.exe is therefore more reliable than using the current JRE directory. This also assumes that the host was installed in the standard location. For non-standard installations, the path to the .jar file should reflect the location of the installation directory.
28 January 2010 Cycle Host User's Guide Revision 1.04 10/59 Deployment Wizard The deployment wizard is the preferred method for configuring an instrument to ensure that all the necessary settings have been properly specified. To start the deployment wizard, type Ctrl-D or select the Deployment Wizard option under the Tools option on the menu bar (see Figure 29). Once the deployment wizard is started, the host will first query the instrument for its current settings. After a brief pause, the first page of the wizard will be displayed. Each of the pages in the deployment wizard will have three buttons at the bottom right for navigating through the wizard. The left button is used to go back to the previous page in the wizard. The middle button is used to proceed to the next page in the wizard. As such, it is typically labeled Next. The right button, labeled Cancel, is used to exit the wizard. It will not cancel previously applied settings. To cancel a pending set of deployment commands, use the Stop| Stop Now button as detailed in the Stop Button section. Deployment Mode
Figure 10: Wizard Operating Mode Options The operating modes page of the deployment wizard asks for the operating mode for the instrument during the deployment (see Figure 10). A brief description of each of the modes is shown next to it's associated radio button. For more detailed information on each of the modes, please refer to the Operating Modes section.
28 January 2010 Cycle Host User's Guide Revision 1.04 11/59 Configuration Settings
Figure 11: Deployment Wizard Configuration Settings The configuration settings page of the wizard is common to all the available operating modes of the instrument (see Figure 11). It offers a number of preselected recommended settings, but also has controls to override the recommended settings if needed. The following sections describe each of the settings in more detail
Synchronize Clock The Synchronize Cycle clock to host Yes option will set the instrument clock to match the host clock at the time when the deployment settings are sent to the instrument. The No option will leave the Cycle clock at its current time and date.
Reset Sample Counter The Reset sample counter Yes option will reset the sample or run counter to 1. This is recommended if a new data subdirectory is to be specified. Resetting the run counter when using an existing data directory could result in multiple sample sequences in a single sample file. Select the No option to leave the sample counter at its current value.
28 January 2010 Cycle Host User's Guide Revision 1.04 12/59 Reset Power Consumption The Reset power consumption Yes option will reset the instruments internal power consumption tracking. The No option will leave it at the current values. It is recommended that the power consumption should be reset each time a new battery is installed, or at each deployment if not running from a battery.
On Board Data Directory
Figure 12: Example Wizard On Board Data Directory Combo Box The on board data directory combo box is used to select the data subdirectory for the upcoming deployment . It is highly recommended that a new directory be specified for each deployment. For that reason, this field is initially empty. The next page of the wizard may not be accessed until an on board data directory has been specified. Selecting the down arrow on the combo box will display a list of the directories that already exist on the instrument. The current data directory will be highlighted (see Figure 12). One of the existing directories may be selected, but a warning message will be issued by the wizard.
Cartridge Volumes at Deployment Each of these fields is used to specify the volumes of reagents in each of the cartridges at deployment time. New cartridges typically contain 250 mL of reagents. The update check box next to each of the deployment volume fields specifies that this new value is to be sent to the instrument. De-selecting an update check box will leave the deployment volume for that cartridge at its existing value. The corresponding field will become un-editable, and display the volume of reagents that the instrument estimates the cartridge currently contains. It is highly recommended that a full set of new cartridges be installed for each deployment. Sampling Schedule Settings The following sections describe the controls on this page of the deployment wizard. If invalid times or dates are specified, the wizard will not proceed to the next page until the errors are corrected.
28 January 2010 Cycle Host User's Guide Revision 1.04 13/59 Figure 13: Deployment Wizard Sampling Schedule Settings Priming Start Date and Time This calendar chooser and time field are used to specify a date and time for the instrument to run a priming sequence. The dates and times prior to the current time are not allowed. The time is specified as hours:minutes:seconds. The hours are specified using 24 hour notation, ie. 1 pm is 13:00:00, and midnight is 00:00:00. Note that the hours, minutes and seconds values may be entered as one or two digits. For example 2:05 pm could be specified as 14:5:0, 14:05:0 or 14:05:00, but not 14:5 or 14:05. When setting these values, be sure to allow enough time for the instrument to be submerged before priming is to begin. With the default priming settings, at least thirty minutes are needed for a priming sequence. If the specified sample start time is less than thirty minutes after the start of the priming cycle, a warning will be issued.
Skip Priming This check box may be used in those rare cases when a priming sequence is not desired. When this box is selected, the priming date and time fields will be disabled.
28 January 2010 Cycle Host User's Guide Revision 1.04 14/59 Sampling Start Date and Time As with the priming date and time fields these controls are used to specify the time and date for the first sample of the deployment. They will not be available if the synchronous slave operating mode is selected. In that case, sample timing is solely controlled by the master device (ie. DH4 or other data logger). When configuring the master device, please ensure that the first sample is at least thirty minutes after the start of the priming cycle.
Number of Samples See the Settings Tab:Sample Settings:Number of Samples section for a description of this field. Unless you have a compelling reason, it is recommended that this field remain blank, instructing the Cycle to continue sampling until it runs out of power.
Sample Interval See the Settings Tab:Sample Settings:Sample Interval section for a description of this field.
28 January 2010 Cycle Host User's Guide Revision 1.04 15/59 Settings Summary
Figure 14: Example Settings Summary Following the sampling schedule page is a textual summary of the settings that will be applied to the instrument(see Figure 14). They are based upon the selections made in the previous pages of the deployment wizard . Those settings that are not recommended will be labeled as such (see the highlighted area in Figure 14 - note that this highlighting does not actually appear within the summary). Clicking on the middle button, which is labeled Send Settings to Cycle on this page, will, as the name implies, send the proposed deployment settings to the instrument. The back button can be used at this point to go back to previous pages and change the settings before the settings are applied. The cancel button can be used to abort the process.
Figure 15: Non-recommended Settings Warning
28 January 2010 Cycle Host User's Guide Revision 1.04 16/59 Figure 16: Settings Report Pop-up
After the Send Settings to Cycle button is selected, a pop-up warning window will appear if any non-recommended settings have been specified (see Figure 15). Finally, before the settings are sent, another pop-up will appear asking if a configuration settings report should be generated (see Figure 16). If Yes is selected, a file browser dialog will appear, requesting the name and location on the host computer where the settings report will be saved. This report is essentially a copy of what appears in the summary window. A file extension is not automatically specified. It is recommended that .txt or .log be used for the extension. It is recommended that a settings report be generated for each deployment to easily track what settings were actually sent to the instrument. Note: Selecting the No button at this point will not prevent the settings from being sent. It will only skip the generation of the settings report. To cancel the settings at this point, use of the Stop Now button (see the Stop Button section) is required.
28 January 2010 Cycle Host User's Guide Revision 1.04 17/59 Settings Results
Figure 17: Deployment Wizard Results with Pop-up The next page of the wizard will display the settings being sent to the instrument. The only button available at this point is the Finish button. Selecting it will close the wizard after a prompt asking to generate a results report (see Figure 17). This report records the new settings that the instrument will use and also the previous state for those settings. By saving a results report, previous settings may be tracked or recovered if erroneous settings were inadvertently applied. If a summary report was generated when the settings were sent to the instrument, a pop-up will ask if the results should be appended to that settings report. Yes is the recommended option, as it keeps a copy of the actual settings with a copy of the intended settings. If a settings report was not generated or no was selected to the append pop-up, a file browser dialog will allow the file name and location on the host computer to be specified. The instrument will then automatically be put into a low power state so that it can be disconnected from its current power supply, transported, connected to its deployment power source and deployed. If an error is discovered in the settings, reconnect the instrument to the host cable, apply power, and select the Stop Now button (see the Stop Button section) to cancel the incorrect sampling schedule. Then start the deployment wizard again to specify new settings.
28 January 2010 Cycle Host User's Guide Revision 1.04 18/59 Main Screen
Figure 18: Cycle Host Main Window The main screen of the host (see Figure 18) consists of a menu bar, a number of controls and indicators across the top portion of the window, a tabbed pane, and a status bar across the bottom of the window. As shown in Figure 18, the host has not yet retrieved any settings from
28 January 2010 Cycle Host User's Guide Revision 1.04 19/59 an instrument. Title Bar
Figure 19: Sample Title Bar
The title bar at the top of the window will initially only show the program name. Once the host has retrieved the settings from an instrument, the serial number of the connected instrument will also appear in the title bar. Once the instrument begins outputting phosphate samples, the most recent sample value, along with it's time and date will also be displayed in the title bar (see Figure 19). COM Settings
Figure 20: Sample COM Settings The COM Settings section at the top left of the main window contains two combo boxes that allow the user to specify the serial port number and baud rate to be used when connecting to an instrument. The first time the program is run, the port number will default to None. When the host program is closed, it will remember the last port used, and automatically attempt to reconnect to that port again the next time the host is run. This auto-connect functionality can be disabled via the Tools|Options menu item. When the host is started, it will automatically search the computer for available ports, and add them to the drop down list in the port number combo box (see Figure 20) for easy selection. A port number may also be set by typing the port number into the text field of the combo box and then hitting enter. If a selected port is unavailable or in use by another program, a pop-up window will appear, and the port
28 January 2010 Cycle Host User's Guide Revision 1.04 20/59 number will revert to None. For information on connecting a Cycle to the host computer, please refer to the Cycle Hardware User's Guide. The host also supports a number of different baud rates, but it is recommended that the default setting of 19,200 be used. The baud rate may be changed even after a com port has been opened. Note that changing the baud rate used by the host does not currently update the baud rate used by the instrument. Instrument Settings Buttons
Figure 21: Instrument Settings Buttons To the right of the COM Settings controls are a group of three buttons that are used to query and update the Cycle instrument settings (see Figure 21). Generally upon first connecting to an instrument, it is recommended that the Get Settings button should be selected (unless the Deployment Wizard is to be run right away). This will update the host with the current state of the instrument. The Apply New Settings button is used to update the instrument settings with any changes that have been made within the host. If there are any pending changes within the host, the area around the settings buttons will be highlighted in yellow until the settings have been applied to the instrument, or until the changes in the host have been reverted to their current settings (see Figure 40). The Clear Changes button may be used to automatically clear any pending setting changes. For more information on the instrument settings, see the Settings Tab section. Time and Date Settings
Figure 22: Time and Date Settings
To the right of the instrument settings buttons is the section with the time and date settings
28 January 2010 Cycle Host User's Guide Revision 1.04 21/59 (see Figure 22). The top line shows the time zone used by the host within parentheses, followed by the the date and time format used by the host. The time zone used by the host is currently the time zone as specified by the Time Zone tab in the Windows Date and Time Properties settings, which can be accessed via the Date and Time option from within the Control Panel. Please contact Wet Labs ([email protected]) if a date or time format other than the default is required. Below the time zone and format line is a line that shows the current date and time of the host computer. Beneath the host date and time is a field showing the date and time on the instrument itself. The instrument time is only updated within the host when the instrument settings are updated via the Get Settings button. Any drift in the instrument time relative to the instrument time as tracked by the host will not be apparent to the host until the instrument settings are refreshed. If the host detects that the instrument time differs from the host time by more than 5 seconds, a pop-up window will appear and present the option of synchronizing the instrument clock to the host clock. The instrument clock may also be manually synchronized with the host computer clock via the Set Date and Time button on the settings tab (see Settings Tab:Controls). Automatic synchronization of the instrument to host clock is also available within the deployment wizard (see Deployment Wizard:Configuration Settings). Operation and Status
Figure 23: Instrument Status and Controls In the top right corner of the host window (see Figure 23) is an area that shows the current operating status, the time to the start of the next scheduled sample, if any, in hours:minutes:seconds, and the time until a priming sequence, if scheduled, also in hours:minutes:seconds. These status indicators will only reflect the actual instrument status after the settings have been retrieved from the instrument via the Get Settings button, or as the host receives data from the instrument after the serial connection has been established. See Table 2 for a listing of the currently available status indicators and their meaning.
28 January 2010 Cycle Host User's Guide Revision 1.04 22/59 Status Meaning Unknown The host has not yet received any information to know what state the instrument is currently in. Sleeping The instrument is in a low power sleep state Idle The instrument is not currently running a sample, and has not yet automatically gone to sleep. It may be executing other commands such as priming, or just waiting for a new command. If no commands are received by the Cycle within it's idle time (see the Idle Time section) it will automatically enter the Sleeping state. The default idle time is 2 minutes. Running A sample is currently running. Table 2: Instrument Status Indicators Below the status indicators are three buttons and a check box that can be used to control the instrument operating state. The Run and Stop buttons are intended for use in laboratory situations. For field deployments, use of the deployment wizard is recommended (see the Deployment Wizard section).
Run Button
Figure 24: Run Options
Selecting the run button will bring up a pop-up window (see Figure 24) that presents the user with the three options and their actions, listed in Table 3.
28 January 2010 Cycle Host User's Guide Revision 1.04 23/59 Button Action Set Start Time/Date Brings up a dialog that allows the user to specify start times and dates for priming and sampling. See the section Sampling Schedule Settings in the Deployment Wizard section for details on the dialog Run Now Command the instrument to immediately start a sample sequence with the current instrument settings Cancel Close the pop-up without starting a sample or specify a start time and date. This is the same operation as clicking on the window close button in the top right corner of the pop-up. Table 3: Run Button Pop-up Options
Stop Button
Figure 25: Stop Options
Selecting the stop button will bring up a pop-up window (see Figure 25) that presents the user with the three options and their actions listed in Table 4. Button Action Stop and Flush Terminate the current sample sequence and execute the flush cycle normally executed at the end of the sample sequence (see the sample sequence section of the Cycle Hardware User's Guide). Stop Now Terminate the current sample sequence immediately with no flushing. This is not recommended unless a new sequence will be started very soon, or if the instrument will be recovered, and a manual flush sequence performed. Continue Close the pop-up without stopping the current sample sequence. This is the same operation as clicking on the window close button in the top right corner of the pop-up. Table 4: Stop Button Pop-up Options
28 January 2010 Cycle Host User's Guide Revision 1.04 24/59 Sleep Button This button will put the instrument into a low power sleep state if it is in an idle state. This button should be selected before removing power to the instrument (either battery or power supply) to prevent accidental loss of instrument configuration settings.
Stop After Sample Check Box This check box enables cancellation of the instrument's current sampling schedule at the end of a currently running sequence, or at the end of the next sequence if the instrument is between samples. Note: this will only operate properly if the host remains connected to the instrument until the end of the sample sequence. Offload Directory Combo Box
Figure 26: Offload Directory Combo Box This combo box (see Figure 26 ) specifies the directory on the host computer where files offloaded from the instrument will be stored. A directory path may be entered manually, or the browse button ( ) to the right of the combo box may be used to open a directory browser dialog. If a directory path entered in the combo box does not already exist, a confirmation pop-up will ask whether it should be created. The drop down list for the combo box keeps track of the directories used during the current session. When the host is closed, it will store the current directory path, and automatically select it as the offload directory the next time the host is run. Status Bar
Figure 27: Com Active Icon The status bar is located at the bottom of the main screen. Offload status messages will appear at the left side of the status bar. At the right side of the status bar is a visual indicator of the com port status. If the port is not connected, the indicator is a static icon. If a port is selected, the indicator is an animated icon (see Figure 27 ).
28 January 2010 Cycle Host User's Guide Revision 1.04 25/59 Menu Bar The menu bar at the top of the main window presents several options for control of the host program. File Menu
Figure 28: File Menu Options Exit This option will cause the host program to close. The current com port in use, the current offload directory on the host computer and the currently selected tab will be stored and automatically retrieved the next time the host is run. This option may also be run by hitting Ctrl+Q or using the window close button at the top right corner of the main host window. Tools Menu
Figure 29: Tools Menu Options Deployment Wizard This option will start the deployment wizard. It may also be started by hitting Ctrl-d.
Get Settings This option will get the current settings from the instrument, just as though the Get Settings button was pressed. It may also be executed by hitting Ctrl-g.
28 January 2010 Cycle Host User's Guide Revision 1.04 26/59 Figure 30: Options Pop-up Window Options This option will bring up the Options pop-up window (see Figure 30), which can be used to control COM port auto-connection at start up, and the maximum allowable PO4 concentration to be shown through auto-scaling in the PO4 plot. Help Menu
Figure 31: Help Menu Options Help Contents This option will display the built-in help files, of which this user's guide is included. It may also be displayed by hitting the F1 key. The F1 key is not yet context sensitive.
About This option displays version information about the host program.
28 January 2010 Cycle Host User's Guide Revision 1.04 27/59 PO4 Plot Tab
Figure 32: PO4 Plot Tab Plot Area The plot area of the PO4 plot tab displays the phosphate concentration as output by the
28 January 2010 Cycle Host User's Guide Revision 1.04 28/59 instrument in µM units versus the time and date of the sample (see Figure 32). Samples received after the com port is connected are plotted automatically. Additional samples may be added to the plot if raw sample files or summary files are "replayed" (see the Files Tab:File Management Controls section for more information).
Figure 33: Plot Display Options A number of plot display options are available through a pop-up menu that may be displayed by right clicking the mouse while the cursor is over the plot area (see Figure 33). The domain axis referred to by the pop-up menu is the time axis, the range axis is the phosphate concentration axis. If the mouse pointer is paused over one of the data points as seen in Figure 32, the time and date of the sample and the phosphate concentration for that point will be displayed in a tool-tip near the point.
28 January 2010 Cycle Host User's Guide Revision 1.04 29/59 Plot Controls
Figure 34: PO4 Plot Controls The plot controls portion of the PO4 plot is hidden by default. To display it, click on the small left pointing arrow at the top of the slider bar at the right side of the plot tab. To re-hide the plot tab, click on the right pointing arrow (seen next to the cursor image in Figure 34). The PO4
28 January 2010 Cycle Host User's Guide Revision 1.04 30/59 plot controls currently consists of a button and a check box. The Clear Plot button is used to clear all the current data points from the plot area. The source data from the instrument will remain unaffected by this operation. The check box controls the display of out of range data (negative or greater than the threshold specified in the Options section). Related to the check box is the number of plotted points indicator in the top left corner of the plot area. The number on the left indicates the number of points greater than or equal to 0.0 and less than the out of range threshold. The number on the right indicates the total number of data points. In Figure 34, it reads 356/356, indicating that all 356 of the points received are within the specified limits. In rare cases, the Cycle may be unable to calculate a phosphate concentration. Should this occur, it will output nan (not a number). Any nans received by the host will be included in the number of points received, but will not be included in the number of valid points, regardless of whether the out of range check box is selected or not.
28 January 2010 Cycle Host User's Guide Revision 1.04 31/59 Raw Plot Tab
Figure 35: Sample Raw Plot
28 January 2010 Cycle Host User's Guide Revision 1.04 32/59 Plot Area The plot area of the raw plot tab displays the raw signal counts, which are proportional to the transmittance, for a sample sequence relative to the sequence start time in hours:minutes:seconds. This plot can be used as a quality assurance tool for monitoring the state of the instrument. Raw data received after the com port is connected is plotted automatically. Additional sequences may be plotted if raw sample files are "replayed" (see the Files Tab:File Management Controls section for more information). A number of plotting options are available through a pop-up menu that may be displayed by right clicking the mouse while the cursor is over the plot area (see Figure 33). The domain axis referred to by the pop-up menu is the time axis, the range axis is the raw signal counts axis. If the mouse pointer is paused over one of the data points, the time of the data point relative to the sequence start time and the raw signal counts value for that point will be displayed in a tool- tip near the point.
28 January 2010 Cycle Host User's Guide Revision 1.04 33/59 Raw Plot Controls
Figure 36: Raw Plot Controls The plot controls portion of the raw plot is hidden by default. To display it, click on the small left pointing arrow on the slider bar at the right side of the plot tab. To re-hide the plot tab, click on the right pointing arrow (seen next to the cursor image in Figure 36). The raw plot controls
28 January 2010 Cycle Host User's Guide Revision 1.04 34/59 consist of a button that can be used to clear all the raw plots from the plot area, and a text field that can be used to control the maximum number of raw plots visible at a time. It is recommended that the maximum number of raw plots be kept below 10 plots to limit plotting overhead. The default maximum number of raw plots is 6. This number is reset to the default each time the host is started. Changes to the maximum number of raw plots will not update until after the current sequence has completed.
28 January 2010 Cycle Host User's Guide Revision 1.04 35/59 Files Tab
Figure 37: Sample Files Tab The files tab is used to manage the data files stored on the flash drive within the Cycle instrument. Its sections are described in detail below.
28 January 2010 Cycle Host User's Guide Revision 1.04 36/59 Instrument File Tree
Figure 38: Unknown Instrument Files The instrument file tree displays the directories and files stored within the instrument (see Figure 37). When the host first starts, it has no knowledge of the current files on the instrument. To reflect this, it will first show a single node labeled Unknown (see Figure 38). Clicking on the Refresh Directory Listing Button will obtain a listing of the instrument's root directory and current data subdirectory as seen in Figure 37. If there are a large number of files in a selected subdirectory, there may be a significant delay before the listing is displayed. Other subdirectories may be viewed or updated by clicking on the + next to the desired directory. Individual files or directories can be selected with a single left click. Multiple files and directories may be selected or deselected by holding down the Ctrl key while left clicking. A range of files/directories may also be selected by left clicking on the first item and then holding down the shift key while left clicking on the last item to select.
Figure 39: Example Empty Subdirectory During Refresh Directories that contain no files, including the data subdirectory, will not expand until they contain at least one file. While being refreshed, empty subdirectories will briefly display an un- labeled sub node (see Figure 39) before collapsing back to an un-expanded directory.
28 January 2010 Cycle Host User's Guide Revision 1.04 37/59 File Management Controls
Cycle On Board Data Dir Controls The on board data subdirectory that the instrument uses to store sample files in is displayed in the Cycle On Board Data Storage Dir field following a refresh of the directory listing. In Figure 37 the data subdirectory is RUN6. The on board data subdirectory can also be manually changed by typing in a new or existing subdirectory. Entries are not case sensitive, but are limited to 8 alphanumeric characters (a-z, A-Z, and 0-9). Hitting the Enter key or selecting the change button will direct the instrument to change the data subdirectory specified in the text field. If the specified directory does not exist, a pop-up confirmation window will query whether the directory should be created. If a directory name of more than 8 characters is entered, a pop-up confirmation will query whether a directory of the first 8 characters would be suitable. Following the directory change, the host will collapse the other directories, and then expand the listing of the new data directory. If it is a new file, the directory will not expand as detailed in the Instrument File Tree section.
Refresh Directory Listing Button This button is used to refresh the files and directories listed in the instrument file tree. This operation can take as long as 20-30 seconds if there are a large number of files within a directory. To verify that a directory listing is in progress, it's OK to switch over to the monitor tab to view the files being listed without affecting the listing.
Offload Selected Files Button This button will sequentially transfer the selected files within the instrument file tree to the host computer. The location of the offloaded file is specified by the Offload Directory Combo Box shown in Figure 26. If a file of the same name already exists in the offload directory, a new copy will be created with a new file name. The new file name consists of the original file name with _nnn appended, followed by the original file extension. The nnn appended is a one up counter that will result in a unique file name. Thus if the files summary.txt and summary_001.txt already exist in the offload directory when summary.txt is again offloaded, it's new name will be summary_002.txt. Gaps in the extension numbering sequence will be filled back in by subsequent offloads. For example, if summary_001.txt is deleted from the directory in the example above, leaving summary.txt and summary_002.txt, then another offload of summary.txt will be copied into the file summary_001.txt. Once the gaps have been filled in, the numbering resumes at the next available number. Each file offloaded is verified to its accuracy by both its length and also by the 32 bit cyclic redundancy code specified in the IEEE 802.3 standard. This should detect 99.999999977% of all possible errors within the file offload. During offload, the file name of the file being written to on the host will include the characters _SUS just before the file extension. Should the offload be terminated early, fail the
28 January 2010 Cycle Host User's Guide Revision 1.04 38/59 CRC check, or fail for some other reason, the _SUS will remain within the file name, indicating that it is a suspect file. When a file is fully offloaded and has passed its CRC, the file will be renamed to remove the _SUS tag. Once a selected file is offloaded and verified, it will be deselected from the file tree. Offload status is reflected both in the status bar and by the "Current File:" field. The status bar will display messages when file offloads are started and finished. The current file field will show the name of the file currently being offloaded.
Replay Selected Files Button This button allows for the data in a file to be added to the plots on the plot tabs without storing it to the host computer. Replay of files on the host computer is not yet implemented. If a sample file is replayed, its data will show up in both the raw plot and also the PO4 plot. If a summary file is replayed, its data will only appear in the PO4 plot.
Cancel File Offload Button This button can be used to cancel a current offload. Data that has already been offloaded will be stored into a normally named file, but will be shorter in length and include the text _SUS just before the file extension. The Wake button on the monitor tab may be used with the same effect as the cancel offload button.
Delete Selected File(s)/Dir(s) Button This button can be used to permanently delete selected files and directories from the instrument. A confirmation window will appear before any files are deleted. A directory cannot be deleted until its files have first been deleted. The current data directory may not be deleted. To delete the current data directory, first specify a new data directory.
File Filter Selection Below the instrument file tree is a drop down list of filters for controlling which of the instrument files are shown in the file tree. This list is currently limited to just *.TXT, which includes all the raw and summary data files. File/Drive Status Indicators Beneath the on board data directory field are several fields that display the free space remaining, used space, and total space on the instrument drive. There is also a "gas gauge" that displays the drive space used relative to the total drive space. Beneath the delete selected file(s)/dir(s) button is an area that displays the host computer offload directory and the name of the file currently being offloaded. The current file field will be blank if an offload is not currently running.
28 January 2010 Cycle Host User's Guide Revision 1.04 39/59 Settings Tab
Figure 40: Example Modified Settings
28 January 2010 Cycle Host User's Guide Revision 1.04 40/59 Controls The controls portion of the settings tab consists of three buttons along the top of the settings tab (see Figure 40). The Set Date and Time button will synchronize the instrument time and date to the host computer. The Flush button is a convenient means for running the sample pump through 500 pump cycles. The Flush button should be used after instrument recovery to flush the system with clean water to prevent fouling. The Prime Now button is used to run the instrument through a priming cycle. It is intended for use in the lab. For deployments, the priming time should be specified using the deployment wizard. Sample Settings The sample settings panel on the settings tab displays a number of instrument settings related to the configuration of the instrument's sampling schedule. The fields within the panel will be filled in once the settings information has been retrieved from the instrument via the Get Settings button. Each of the settings is displayed in two columns. The left column shows what the current instrument settings are. The right column initially displays the current settings, but its values can be changed to modify the current settings. As described in the Instrument Settings Buttons section, changes to the sample settings that have not yet been applied to the instrument will cause the area around the instrument settings buttons to turn yellow (as seen in Figure 40). Changes to the right column fields are detected by the program when the focus changes to another component via a mouse click, a press of the Tab key, or a press of the Enter key. Those values that have been changed from their current settings will also have yellow backgrounds until the new settings are applied or reverted to the current setting (see the Num Samples and Idle Time fields in Figure 40). All the settings within this section are also configurable within the deployment wizard. They are displayed here for use in deployment planning with the deployment calculator (see the Deployment Calculator section). Below are descriptions for each of the fields in the sample settings panel.
Sample Interval The sample interval determines how frequently the instrument runs a sample, by specifying the time from the start of one sample sequence to the start of the next sample sequence. When setting this field, keep in mind the time that is actually required for a sample sequence to complete. The instrument will run a sequence to completion, regardless of the interval setting. If the interval has passed before a sequence is completed, the following sample sequence will begin as soon as the previous sequence has completed. The value entered into the interval field is in the format hours:minutes:seconds. For intervals longer than one day, simply convert the number of days to hours. For example, to have the instrument run samples every other day, the interval would be 48:00:00. Note that the minutes and seconds values may be entered as one or two digits in the range 0 to 59. The hours value may be as one or more digits in the range 0 to 1000. For example, an hourly schedule could be entered as
28 January 2010 Cycle Host User's Guide Revision 1.04 41/59 1:0:0, but not 1:0 or 1:0: . The default setting for the sample interval is one hour (1:00:00).
Number of Samples The number of samples field is used to limit the number of sample sequences that are executed following the use of the Run Now button, or a run scheduled by a start date and time. The number of samples can be set from 1 to 32767 sample sequences, or if the field is set to -1 or left blank (as seen in the pending number of samples field in Figure 40), the instrument will continue to run sample sequences as long as it has power, or until it is stopped, regardless of whether it may have depleted the contents of its cartridges. The default setting for the number of samples is a blank field, indicating the unlimited sampling option.
Idle Time The idle time setting in hours:minutes:seconds determines how long the instrument will "stay awake". If there is no activity on the instrument's serial port within the specified idle period following a sample sequence or a command, it will revert to it's low power sleep state until the next scheduled sample sequence or until the instrument is awakened. Changes to this interval can greatly affect the power consumed by the instrument over the length of a deployment, so it is advisable to set it to less than the default value of two minutes. Likewise, setting the value to less than three seconds can result in unresponsiveness of the instrument.
Prime The prime check box can be used to show the effects of a prime cycle on the deployment calculator. It does not actually schedule a priming sequence. That must be done via the deployment wizard, or the Run|Set Start Time/Date dialog. Deployment Calculator The deployment calculator shows estimates of the effects of the current and proposed instrument settings on the volumes of reagents used, total effluent output, current consumed (assuming a steady 12V input), and the maximum number of runs that can be executed based upon chemical usage or the number of samples setting. Pump Controls The pump controls, located at the lower left corner of the settings tab (see Figure 40) are provided to allow manual pumping of the sample and chemical pumps. There is generally no need to use these controls, except when flushing an instrument of the red reagent (R2) prior to shipment (see the Preparation for Returning a Cycle to Wet Labs section of the Cycle Hardware User's Guide). The check boxes are used to select which pumps are to be pumped.
28 January 2010 Cycle Host User's Guide Revision 1.04 42/59 The num pumps field is used to specify the number of times that the selected pumps are to be pumped. The Run Pumps button will start execution of the selected pumps for the specified number of pumps. Changes made to the pump selection check boxes or the number of pumps after a run pumps session has been started will not take effect until the next session. The Stop button is used to stop a pump session before it has completed. To monitor the number of pumps remaining in a pumping session, issue the $PMP command with no arguments from the monitor tab.
28 January 2010 Cycle Host User's Guide Revision 1.04 43/59 Status Tab
Figure 41: Sample Status Tab The status tab is used to display the estimated volumes of chemicals in each of the instrument's cartridges (see Figure 41). These volumes are updated when the Get Settings button is selected, or when the Refresh button on the status tab is selected. The host does not estimate changes to these levels as samples execute. To be sure that the levels displayed are current, use the Refresh or Get Settings button.
28 January 2010 Cycle Host User's Guide Revision 1.04 44/59 Monitor Tab
Figure 42: Sample Monitor Tab The monitor tab (see Figure 42) provides a view into the underlying serial data between the host and the cycle instrument. It is generally not used, but is very useful for debugging
28 January 2010 Cycle Host User's Guide Revision 1.04 45/59 unexpected operation. It consists of a scrollable text area that shows the serial traffic, a text field for manually entering instrument commands, and Send and Wake buttons. The text area is not editable, but sections of it can be selected by clicking and dragging with the left mouse button held down. The entire area may be selected by typing Ctrl-A on the keyboard after the monitor text area has been selected with a single left mouse click. A selected text area may be written to a file on the host computer via a pop-up menu. The pop-up is activated by right clicking within the text area and choosing the save selection option (seen next to the cursor image in Figure 42). The text area retains the last 5,000 lines of serial data. It can be cleared by the clear monitor option of the text area pop-up menu. Also available from the pop-up menu is the Find option which provides case sensitive searching of all the text within the monitor. Manual commands to the instrument can be typed into the command text field below the monitor text area. Commands are sent to the instrument when the Enter key is pressed while typing the the command text field, or when the Send button is clicked. The Wake button can be used to send an RS-232 break signal to the instrument to wake it up from a sleep state.
28 January 2010 Cycle Host User's Guide Revision 1.04 46/59 Additional Items Hot Keys Hot Key Function F1 Display help file contents Ctrl+D Run deployment wizard Ctrl+G Get settings Ctrl+Q Exit the host program Table 5: Hot Key Functions Table 5 lists the available hot keys and their associated functions. Although the keys are shown in uppercase, the Shift key should not be used. Session File
Figure 43: Sample Session File
The session file is used to store the COM port and host data directory information for the next session. It is an extended markup language (XML) file that is stored in the
28 January 2010 Cycle Host User's Guide Revision 1.04 47/59 WETLabs\CycleHost subdirectory of the user's application data directory. A sample session file is shown in Figure 43. On Windows XP, the path is C:\Documents and Settings\Username\Application Data\WETLabs\CycleHost\CycleHost.sessi on.xml On Windows Vista, it is C:\Users\Username\AppData\Roaming\WetLabs\CycleHost\CycleHost.session.xml where Username is the Windows login name that the host is currently running under.
28 January 2010 Cycle Host User's Guide Revision 1.04 48/59 Operating Modes There are five major operating modes for integrating the Cycle instrument into a system. Regardless of which mode the instrument is operated in, the raw data and engineering units for each sample sequence are stored on the Cycle's internal flash disk for post-deployment retrieval. The specifics of each operating mode are listed below. Host Controlled Mode In this mode, the instrument is connected to host computer and all aspects of operation are directed and monitored via the Cycle Host Program. This method of operation give the user the best visualization of the instrument and its functioning. Autonomous Mode The autonomous mode, as opposed to the commanded mode, requires the least amount of system integration work. The autonomous mode, as opposed to the commanded mode, allows Cycle to run by itself, connected to nothing more than a power source. To prepare for deployment in autonomous mode, use CycleHost to configure the sample settings for the instrument, then put the instrument into a low power sleep state. The instrument can be disconnected from the host computer at this point, and it will remain in sleep mode until the programmed prime and sample times. During this period, it can be transported to the deployment site, connected to its power source and deployed. Example 1 The Cycle is to be installed on a mooring that has no controller or data logger. Its power is to be supplied from a dedicated battery pack. In this case, the Cycle should be configured for autonomous mode via the deployment wizard. The wizard will take care of configuring all the necessary settings using the steps below. 1. Install new cartridges. 2. Connect the instrument to a 12V, 15W power supply and host computer using the supplied host cable. 3. Start the host program and choose the appropriate serial port. 4. Turn on the power supply. 5. Click on the Get Settings button on the host program and ensure that the host program is able to communicate with the Cycle.
28 January 2010 Cycle Host User's Guide Revision 1.04 49/59 6. Select Tools|Deployment Wizard from the host program menu bar. 7. Choose autonomous mode on the first page of the wizard and click the NEXT button. 8. Proceed through the deployment wizard steps. After clicking on the Finish button on the last step of the wizard, select the yes option to put the Cycle into low power sleep state. 9. Verify that the Cycle status in the top right corner of the host reads Sleeping. 10.Disconnect the host cable from the instrument. Install the instrument on the mooring and connect it to the battery pack. 11. Deploy the mooring. 12.Recover the mooring. 13.Remove the Cycle from the mooring and connect it to the host computer and power supply using the host cable. 14.Power the Cycle. 15.Select the Refresh Directory Listing button on the Files tab. 16.Offload the summary.txt file and any other desired files from the current data subdirectory. Asynchronous Slave Mode The asynchronous slave mode of operation is intended for moored operations where the instrument is connected to a master controller. In this mode, the instrument priming and sampling schedule is configured as if it were to be deployed in autonomous mode, but once configured, the Cycle is connected to the master controller. The master controller will then periodically switch the external wake line to the instrument from a low level of 0 V to 3.3 V to a high level of 3.5 to 20 V, directing the instrument to output its most recent sample value. To ensure proper operation, the master controller should provide continuous power to the instrument on its power line. The wake signal need only remain high for 500 ms before being set back to a low level. The data output by the Cycle in response to each rising edge of the external wake line is specified in the Engineering Units Measurement section. As the asynchronous name implies, the instrument's sample timing is asynchronous to the master controller. It runs on its own predetermined schedule, independent of the master controller or other instruments within the system. The master controller should issue a rising edge of the wake line at an interval that is at least half the sampling interval of the Cycle's sampling interval (in other words, at least twice the frequency) in order to effectively record all the sample data at the master controller.
28 January 2010 Cycle Host User's Guide Revision 1.04 50/59 Example 2 The Cycle is to be installed on a mooring with a system controller that will be set to collect and forward sample data to a shore side database every 15 minutes. The other instruments on the mooring will be turned on for 2 minutes every quarter hour before the data is transmitted. The sampling interval for the Cycle is to be hourly. The controller has a number of instrument data ports, but only one switched power line. In this case, the recommended operating mode is the asynchronous slave mode, because the sampling and power frequency for the other instruments is shorter than the time required for Cycle to perform a measurement. The asynchronous slave mode also allows the controller to treat the Cycle just as it does the other instruments on the mooring by switching the power line to the Cycle's external wake line while switching the power on to the other instruments. Power to the Cycle is supplied directly from the system's battery, "upstream" from the controller's instrument power switch. The periodic switching of the power to the other instruments will cause the Cycle to output it's most recent sample data to be collected and forwarded with the other instrument data, but still allow Cycle to continue on it's own hourly sampling schedule. Cycle should be configured via the deployment wizard. The wizard will take care of configuring all the necessary settings using the steps below. 1. Install new cartridges. 2. Connect the instrument to a 12V, 15W power supply and host computer using the supplied host cable. 3. Start the host program and choose the appropriate serial port. 4. Turn on the power supply. 5. Click on the Get Settings button on the host program and ensure that the host program is able to communicate with the Cycle. 6. Select Tools|Deployment Wizard from the host program menu bar. 7. Choose asynchronous slave mode on the first page of the wizard and click the next button. 8. Proceed through the deployment wizard steps. Choose priming and sample start times that allow for adequate time to deploy the mooring. After clicking on the Finish button on the last step of the wizard, select the yes option to put the Cycle into low power sleep state. 9. Verify that the Cycle status in the top right corner of the host reads Sleeping. 10.Disconnect the host cable from the instrument. Install the instrument on the mooring and connect its power line to the battery pack and it's external wake line to the switched power line that runs the other instruments. 11. Deploy the mooring.
28 January 2010 Cycle Host User's Guide Revision 1.04 51/59 12.Recover the mooring. 13.Remove the Cycle from the mooring and connect it to the host computer and power supply using the host cable. 14.Power the Cycle. 15.Optionally select the Refresh Directory Listing button on the Files tab and offload the summary.txt file and any other desired files from the current data subdirectory. Synchronous Slave Mode The synchronous slave mode operates in a similar mode to the asynchronous slave mode, but in this case, the external wake line is used by the master controller to initiate a sample sequence, rather than control the output of data. When the instrument detects a rising edge of the external wake line, provided a sample is not already running, it will begin a sample sequence. Depending upon the output mode setting (SDO), the instrument will output data as configured until reaching the end of its sample sequence. It will then wait for the next rising edge of the external wake line to begin a new sample sequence. This mode is considered synchronous because its sampling is synchronized to the master system. As with the asynchronous mode, in this mode, the master controller should provide continuous power to the Cycle via it's power line. Example 3 The Cycle is to be installed on a mooring with a system controller that will be set to collect and forward sample data to a shore side in real-time. The controller is capable of being reprogrammed in-situ to allow for more or less frequent sampling. It is also desired that the instruments all sample at the same times. In this case, the recommended operating mode is the synchronous slave mode. This mode is chosen in order for the controller to be able to control the sampling interval for the Cycle and to keep it synchronized to the controller clock and the other instruments. Power to the Cycle is supplied directly from the system's battery or from a controller instrument port that can be left on all the time. The Cycle's external wake line is then connected to another instrument power port that is switched on when a sample sequence is desired. Cycle should be configured via the deployment wizard. The wizard will take care of configuring all the necessary settings using the steps below. 1. Install new cartridges. 2. Connect the instrument to a 12V, 15W power supply and host computer using the supplied host cable. 3. Start the host program and choose the appropriate serial port. 4. Turn on the power supply.
28 January 2010 Cycle Host User's Guide Revision 1.04 52/59 5. Click on the Get Settings button on the host program and ensure that the host program is able to communicate with the Cycle. 6. Select Tools|Deployment Wizard from the host program menu bar. 7. Choose synchronous slave mode on the first page of the wizard and click the next button. 8. Proceed through the deployment wizard steps. Choose a priming start time that allows for adequate time to deploy the mooring. The wizard will not prompt for a sample start time, as that aspect will be controlled by the system controller using the external wake line. After clicking on the Finish button on the last step of the wizard, select the yes option to put the Cycle into low power sleep state. 9. Verify that the Cycle status in the top right corner of the host reads Sleeping. 10.Disconnect the host cable from the instrument. Install the instrument on the mooring and connect its power line to the always on power port, and it's external wake line to the switched power port for controlling the Cycle sampling . 11. Deploy the mooring. 12.Update the controller sampling schedule as needed, but still allow enough time for each of the Cycle sample sequences to fully complete before attempting to start the next sample sequence. 13.Recover the mooring. 14.Remove the Cycle from the mooring and connect it to the host computer and power supply using the host cable. 15.Power the Cycle. 16.Optionally select the Refresh Directory Listing button on the Files tab and offload the summary.txt file and any other desired files from the current data subdirectory. Commanded Mode This is the most comprehensive and complete operating mode. In this mode, the instrument is connected to master controller (i.e. host computer or system controller), and all aspects of operation are directed and monitored via the Cycle Command Set. While this method offers the most control of the instrument, it is also requires the most development work to implement.
28 January 2010 Cycle Host User's Guide Revision 1.04 53/59 Output Formats This section contains descriptions of the formatting of data output by the Cycle. The fields are all separated by a single tab character (0x09), which are shown here as single space characters. Engineering Units Measurement The engineering units measurement is recorded at the end of each raw sample file and also in the deployment summary file. It is output at the end of a sample sequence in most of the output modes, and in response to a GLSO command. The date, time, and step fields are fixed width, the others are variable width. The fields are all separated by a single tab character (0x09), which are shown here as single space characters. Also note that in the current version of the firmware, the line that is output as a result of the GLSO command ends with two pairs of
28 January 2010 Cycle Host User's Guide Revision 1.04 54/59 Field Description mm/dd/yy The sample date hh:mm:ss The sample time Run The run counter. It increments by one for each sample sequence run. CAPO4 The micromolar phosphate value to three decimal places, calculated using the instrument's constant a* value (scale factor). May also be nan, -inf, or +inf VAPO4 The micromolar phosphate value to three decimal places, calculated using the instrument calculated variable a* value. May also be nan, -inf, or +inf VAS The variable a* value to three decimal places, used to calculate vapo4. May also be nan, -inf, or +inf State The last step reached in the sample sequence (see Table 7) Flush1 The mean of the last 10 transmittance signal counts in the ambient flush (State = 1) portion of a sample sequence. Amb Min The mean of the 6 transmittance signal counts that triggered the knee slope threshold in the reaction (State = 3) portion of a sample sequence. Flush2 The mean of the last 10 transmittance signal counts in the ambient flush prior to a cal spike (State = 6) portion of a sample sequence. Cal Min The mean of the 6 transmittance signal counts that triggered the knee slope threshold in the reaction (State = 8) portion of a sample sequence. Remaining The number of remaining samples as set by the NOS command. DIAG1-2 Reserved diagnostic fields Table 6: Engineering Units Measurement Fields
28 January 2010 Cycle Host User's Guide Revision 1.04 55/59 Raw Transmittance Measurement The raw transmittance measurement is recorded in the raw sample files and output during a sample sequence when running in output mode 0 (SDO). The frequency of the raw transmittance measurement is by default the average of 5 raw samples. This can be changed via the OPD command. The sig, temp, run, and rc fields are variable width fields, the others are fixed width. The fields are all separated by a single tab character (0x09), which are shown here as single space characters. mm/dd/yy hh:mm:ss sig temp run idx code pc vbat
Index Step Index Step 0 Initial flush 5 Mid flush 2 1 Ambient Read 1 6 Ambient Read 2 2 Mix ambient 7 Mix spiked 3 Ambient PO4 8 Spiked PO4 Read Read 4 Mid flush 1 9 End flush Table 8: Index Field to Sample Sequence Step State
28 January 2010 Cycle Host User's Guide Revision 1.04 56/59 File Formats Summary File Format The Cycle summary files are ASCII text files that reside on the Cycle instrument and contain summary sample information for all the samples within each on-board data sub-directory. When new data sub-directories are specified for each deployment, the summary file will contain the summary data for each deployment. Each summary file starts with a tab separated header line containing the following text (tabs shown as spaces), terminated by a linefeed,
28 January 2010 Cycle Host User's Guide Revision 1.04 57/59 Field Description ver:v.vv The firmware revision number (v.vv) that the file was collected under av=aa.aa The pump volume stored by the Cycle for the ambient pump volume (aa.aa) in µL cv=cc.cc The pump volume stored by the Cycle for the calibration pump volume (cc.cc) in µL r1v=yy.yy The pump volume stored by the Cycle for the R1 reagent pump volume (yy.yy) in µL r2v=rr.rr The pump volume stored by the Cycle for the R2 reagent pump volume (rr.rr) in µL zo=z.zzzz The zero offset stored by the Cycle (z.zzzz) in µM co=o.ooo The calibration pump volume offset stored by the Cycle (o.oooo) in µL o cas=ss.ss The constant a* value stored by the Cycle (ss.ss) st=t.ttt The slope threshold, which is usually negative, stored by the Cycle (t.ttt) cc=10.53 The calibration standard concentration stored by the Cycle. ups=u The UPS counter stored by the Cycle. It will increment each time power is removed from the Cycle when it is not in a low power sleep state. Table 9: Raw File First Header Line The second header line consists of the following text, with the fields separated by tab characters (0x09). Date Time Signal Temp Run Step Code Counts Vin Each raw file will also typically end with a line that follows the Engineering Units Measurement format following the Raw Transmittance Measurement lines. It too is terminated by a single linefeed ,
28 January 2010 Cycle Host User's Guide Revision 1.04 58/59 Revision History Revision Date Revision Description Originator 1.0 06/18/09 Initial Draft User's Guide B. Rhoades 1.01 7/21/09 Updated Installation Content B. Rhoades 1.03 11/13/09 Updated for Host Release 1.03 and Vista Installation B. Rhoades 1.04 01/28/10 Updated Engineering Units Measurement Table B. Rhoades
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