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1. Initialize2 string are added to the queue nable Disable Controls l Initialize q While G clamp vi execution consequently proceeds with the Enable Disable Controls case 1t suffices here to say that this case will set the enabled state of G clamp vi front panel controls in accord to set parameters for the IV Relation experiment module The precise working of the Enable Disable Controls case is explained in section 4 1 4 4 1 2 Initialize2 1 G clamp vi next retrieves the settings used last for usage and scaling of the analog in and analog out channels These are stored in the values of the controls AI Cluster and AO Cluster of G clamp IIb AnalogInOutConfig vi Thus a VI reference is opened to AnalogInOutConfig vi and the method Get Control Value is invoked on the controls AI Cluster and AO Cluster The obtained strings are unflattened and the retrieved settings are stored in the corresponding cluster element AI Cluster and AO Cluster of the large cluster that is passed from one iteration of the outer While Loop to the next via the top shift register Page 11 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide Ie A ar Cluster ko cluster i pjt m a Control Mame AnaloginOutConfig vi Type Descriptor 3 AI Cluster Get Control value t Control Mame Type Descriptor Al Cluster of the large cluster also c
2. The VI is not executable when finally trying to execute NewModule vi by calling it with G clamp vi it might have been that other copies of Embedded llb with different directory paths on the host computer resulted in incorrect path information to NewModule vi s sub VIs In this case use the File gt Save with Options as outlined on all custom sub VIs of NewModule vi Start with the custom sub VI lowest in NewModule vi s VI hierarchy and work upwards through the hierarchy to the top level VI 1 e NewModule vi Page 65 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide i gt Menu Editor D LabYIEW 6 1 G clamp G clamp ilb G clamp rtm xx File Edit Help lolo Custom Preview File Function Help Item Properties Preferences Data Directory Item Type PxlI Target serie E DAQ Board Configuration Ther N em Mame HewModule Function Item Tag TW Relation md syn Threshold NewModite Synaptic aain la e Enabled Checked 7 Help Shortcut Press key combination About G clamp IS About LabVIEW hi Close the menu editor and save the changes In the Enable Disable Controls case add a new element to the 1 D array of clusters constant that holds experiment module specific display properties for many front panel controls Scroll to the array element corresponding to the new experiment module Exp module C D
3. s Guide 6 Priorities and execution systems While the experiment module VI and thus the communication loop operate under normal priority the feedback loop following general LabVIEW RT programming guidelines executes with the highest priority level time critical priority This can be achieved by setting either the feedback loop module G clamp DQA vi to this priority level or by setting the caller of G clamp DQA vi the Sub vi within the experiment module VI to this level as sub VIs automatically execute at the priority level of the calling VI 1f the priority level of the calling VI 1s higher than the priority level of the called sub VI In the G clamp distributions v1 1 to v1 1 2 it is the Sub vi within the experiment module VIs that have been set to time critical to ensure that not only the feedback loop itself but also the timing between consecutive data acquisitions iterations is under the strictest timing control While this makes sense as far as the five priority levels from backgound to time critical are concerned it 1s unclear from National Instruments Application Note 144 Using LabVIEW to Create Multithreaded VIs for Maximum Performance and Reliability how the priority level subroutine fits in under the conditions of a time critical process running under the real time operating system of the PXI controller We have found that setting all sub VIs used by G clamp DQA vi LabVIEW system VIs and
4. In the case for processing IV Relation data of Process the insertion of Stop into the queue has been deleted as it is unnecessary Page 83 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide G clamp llb G clamp vi In the Exit case the string array constant used at the TRUE case of Select has been changed to Abort index 0 and Done index 1 Before that change index 0 Send control values caused needless execution of the default case Check Controls and index 1 Stop alone 1s insufficient to terminate an ongoing experiment Embedded llb List Templates vi The default value of the control Output channels has been changed from 0 to 0 1 to achieve resetting of both analog output channels present on most NI DAQ boards Embedded llb List Templates vi Using a pre initialized 1 D array of cluster with Replace Array Subset for the conductance settings in the first For Loop has been replaced by a conditional Build Array that depends on the found output of ReadKey vi With the old implementation array size depended on how many conductance module VIs were found by Create Plugin List vi in Embedded llb while it should depend on the number of conductance module entries in Embedded cfg The location of the conductance module VIs has been changed They are no longer located in the library Embedded llb They are now located in the sub directory gModules of c
5. Waveform Graph with the contents of Output Array which acts as buffer for all T futput Array EII acquired traces Because Output Array 1s a 2 D array and Waveform Graph a 1 D array the traces have to be re organized In the resulting 1 D array the first half of elements are the voltage traces and the second half of elements are the current traces In the following For Loop the first half of traces plots is assigned to left voltage y scale of Waveform Graph and the second half of plots to the right current y scale In addition each current trace 1s given the same color as its corresponding voltage trace These operations result in constant updating of the front panel display which can be annoyingly slow and time consuming even with relatively small data sets To speed up this process Auto scaling of the x axis 1s disabled during these operations and minimum and maximum of the x axis of Waveform Graph are set to display only a fraction of the actual data and after all plot operations have been performed the x axis is set back to its original range Page 31 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide Waveform Graph Waveform Graph T e 1 b y 1 DUE BD y NN y 23 Scale ScaleFit P 7 Scale ScaleFit Of XScale ScaleFit as 0 000 H xScale Range Hu 4 1 16 Exit Saves the current settings for the virtual conductances so that thes
6. first element out m 100 name unnamed FIFO 1 fe p yo e fm ro Sd FIT MA FT ee RT RT ET ATFIFO Create vil IRTRIFO rite vi JATFIFO Read vil JATFIFO Delete vi Simple Error Handler wi Figure 2 A Very Simple RT FIFO Example Creating an RT FIFO An RT FIFO is created using the RTFIFOCreate VI The type of elements that the RT FIFO will contain is determined by type of the data wired to the type input terminal the RT FIFO VIs are polymorphic All of the elements in an RT FIFO must be of the same type RT FIFOs can be created of elements of the following types Double Single 18 116 132 U8 U16 U32 RT FIFO elements can also be arrays of the same types as listed above To specify the size of the arrays in each RT FIFO element first wire an array to the type input terminal then wire the size for the arrays to the elements in array input terminal The reference output for the RT FIFO rt fifo is a cluster and will be pink for RT FIFOs with array elements In Figure 3 an RT FIFO called FIFO 1 is created that contains array elements In this case each array element has 5 elements Page 72 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide Array Constant Figure 3 Creating an RT FIFO of Array Elements The RT FIFO is fixed length and the memory for the RF FIFO is allocated when the RT FIFO is created If the RT FIFO was of unlimited length then it would have to dynamically allocate more memory
7. Analogous changes were done in IV Relation Sub vi and V clamp Sub vi Embedded Ilb Gysn Threshold vi and Embedded IIb Gysn Threshold Sub vi Instead of using read gsyn vi in Gsyn Threshold vi and in Gsyn Threshold Page 87 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide Sub vi 1 e read the template file twice read gsyn vi is now used once in Gsyn Threshold vi and the RT FIFOs Result Data Queue and Control Values are used to get all necessary information into Gsyn Threshold Sub vi Information about processor speed and DAQ device has been taken out of the clusters AI Cluster and AO Cluster respectively This information is now transmitted to VIs executing on the PXI controller via the cluster PXI Target Thus in the Initialize case of G clamp vi the method Set Control Value is used to provide List Templates vi with PXI Target and in the Start ExpModule Step2 case of G clamp vi PXI Target is converted to a variant and added to the array of variants successively transmitted to the experiment module VI via Set Control Value VIs affected by this change o in G clamp llb G clamp vi AnalogInOutConfig vi o in Embedded llb List Templates vi IV Relation vi IV Relation Sub vi Gsyn Threshold vi Gsyn Threshold Sub vi Synaptic Gain vi Synaptic Gain Sub vi V clamp vi V clamp Sub vi DAQ Hardware Settings vi Embedded llbiSynaptic Gain vi EOF requiring Open Fil
8. G clamp Programmer s Guide 4 In the Enable Disable Controls case also add a new element to the 1 D array of clusters control ControlsBuffer This control stores the last user control settings when the user switches to another experiment module so that the settings can be restored when the user switches back to the first experiment module This is a hidden control normally not visible on the front panel First make it visible by right clicking while pointing on the terminal and selecting Show Control in the upcoming menu On the front panel scroll to the right array index and set the controls to values that you would like to show up when the experiment module is switched to for the first time after z0000 0 d 1 000 I 0 000 0 0 0 000 d 10 d 1 000 Too 0_5K GTY R 10K GTY i 5K GTY 1K GTY 1PRIMARY GTY 1RC_PRIM GTY 20K GTY 2 10M5 GTY 2 15M5 GTY 0 000 110 000 starting G clamp vi To make these settings permanent right click while pointing on the control select Data Operations gt Make Current Value Default and save G clamp vi In the Start ExpModule Step1 case If the new experiment module uses template files include the new module into the check whether a template has been selected before Insert Queue Element vi receives the string Start ExpModule Step2 If necessary also Selected templates add a case to the Case Structure that replaces individual e
9. Real Time applications such as PID control Assuming that the functionality is enabled in the NI RT INI file for the RT Engine Al SingleScan behaves differently in LabVIEW Real Time than in LabVIEW for Windows There is also a similar VI in the intermediate DAQ Analog Input palette This version of the VI just calls Al Single Scan and has the same inputs except data in Using the Wait and Wait Until Next ms Multiple functions a LabVIEW Real Time programmer can achieve loop rates with sleep modes of 1000 Hz at best A user can achieve higher loop rates but this would be done without sleeping at all However a new functionality of Al SingleScan for LabVIEW Real Time allows the analog input scanclock to control when a thread sleeps and wakes up This also gives a sleeping resolution finer than 1 millisecond After a DAQ board is configured for nonbuffered input at a certain scan rate and is ready to begin sampling the hardware scanclock controls the timing of analog to digital A D conversions Each time the scanclock pulses the board performs an A D conversion for every channel in the scan list and generates an interrupt that is handled by the Al SingleScan VI in LabVIEW Real Time The DAQ board stores the data from the scan in its hardware FIFO buffer Meanwhile the thread from which the Al SingleScan VI was called wakes up when the interrupt is detected and the Al SingleScan VI acquires the data from the hardware FIFO buffer The rest of the code i
10. Status Using the Data Remaining Parameter The data remaining output can be used to monitor whether or not an application is keeping up with the data coming into the FIFO When using the Read oldest data opcode if the FIFO had been initially cleared on the first iteration by using read newest data then each new scan will also be the oldest and after each call of Al SingleScan the FIFO should be empty and the data remaining output should be zero indicating that data is not remaining in the FIFO If for some reason the program does not keep real time Al SingleScan is called with read newest data and there are one or more scans in the FIFO then the data remaining output will be 1 indicating that your program did not keep real time Verifying the Sleep Mode Configuration You can verify that this sleeping functionality is enabled by looking for the following entry in your NI RT INI file associated with the target you are executing code on NI DAQ Page 78 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide UseSleepingTimedNonBuffered TRUE This entry is present by default for all networked LabVIEW Real Time Series PXI Controller targets Networked LabVIEW Real Time Series PXI Controller s NI RT INI files can be found in C NI RT INI of the target s hard drive The Al Single Scan sleep mode is not turned on by default for the 7030 family LabVIEW Real Time Series DAQ devices in LabVIEW RT 5 1 2 but is turned on by default in LabV
11. Vi o da 50 TELS Write to Disk Mods dba 52 7 3 A ota alee dp lestaneteasdad see doootoed E So laeaea eae 54 Page 2 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 7 3 1 VEGAN SOE A e A AA 55 a rete ets Ret Ca ean epee ee Cre en a oy ee cree a ee 56 8 1 AMA SMO UIC OMI ML s 56 8 2 Lit Templates Vd S6 8 3 AVC COMO i 59 8 4 A AO 60 8 5 o A ceva inne eee een eee 62 9 Adding anew experiment module ada dai 64 9 1 CAC A dos dos ad 64 9 2 Adding the module to G ClaMp V1 ooooooonnnnnncnnncononononnnnnnnnnnnnonnnonnnnnnnnnnnnnnnnnnnnnss 65 9 3 NEW CONTO L parameters A Inia 70 10 Non Lab VIEW lesa 71 OE A A E 71 10 2 Read Time Stamp Counter Tunari idad iii 74 HOGS oo E Dale ora 75 11 LabVIEW RTS POCOS A i 76 Mick ATSimolescais SICCPUNOUS id 76 12 Ie TOMES NTE WA sad 79 122 REVISO taa na 81 Page 3 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 1 Who should read this guide This guide is intended for G clamp users who have a basic knowledge of LabVIEW programming though not necessarily of LabVIEW RT and who want to develop a custom experiment module or to make other program modifications The document focuses upon the operation of the main VIs G clamp vi and the experiment module VIs and their custom sub VIs To illustrate how G clamp works we follow program flow during an experiment This approach takes the reader through essential elements within the wiring diagrams It also explains
12. all acquired traces in the front panel waveform graph see section 4 1 15 Plot all and optionally for saving the data to a file Page 26 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 3 Data are written to file if two conditions are TRUE The earerorm orapn front panel control Save data is set to TRUE and the experiment module VI has performed the user specified number of iterations Thus data to be saved accumulate in temporary buffers until the end of the experiment Also while the control Save data 1s read out each time the Process case executes it matters only at the end of the experiment when the last set of data is processed Filenames for the data file are created by the sub VI GetDatafileName vi in the TRUE case for saving data GetDatafileName vi uses the Get Date Time In Seconds function to get the current time when it executes Date and time are converted to a string which includes the proper file type extension for the selected experiment module using Format Date Time String Thus date and time in the file name reflect the end of the experiment Experiment module specifics IV Relation The operations necessary to obtain the relation between injected current and membrane potential are straightforward and easy to figure out The two 1 D arrays of DBLs Voltage and Current provide the xy graph IV Relation with input and serve as buffers before the data get saved to fil
13. an Index Array which uses the variable Exp Type set in the Menu Selection User case of the Event Structure in the default case Check Controls to index the array samp ble otal number Disabled e Controls Page Enabled State E Page Enabled 1 Mi ELE cycle tine Disabled leak Period Visible zweep duration Disabled Hinicabiled IN Y i al fomin 1 Gmaxfz Visible sample rabe Disabled _botal number Md total number Disabled 5 scaling 2 Gm Caption Text HF Show traces Visible Gmax 2 Caption Text Jl i Show traces Wisible___ Misible f Threshold Visible k fa 2 un q Em E Period bo use For Disabled alculati gF lear i a Ji IET E PageEnb E e o Other experiment module specific control properties that are set by the user the cluster of controls in the right part of the Settings page which also contains hidden controls to buffer the values of the controls Gmin 1 Gmax 2 and Available templates are stored in the 1 D array of cluster ControlsBuffer Available templates Disabled hems TE 4 E i pe cwn z Gmaxf22 Valuer oes il ee mals l ANETTE Template Files Page 16 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 4 1 5 PXI Target This case is invoked by the menu item File gt Preferenc
14. any changes in the cluster indicators AI Cluster and AO Cluster permanent and allow G clamp vi during initialization to obtain the information about the last PXI controller by invoking the method Get Control Value on the AI Cluster and AO Cluster indicators of AnalogInOutConfig vi see 4 1 2 Initialize2 8 2 List Templates VI In Embedded llb List Templates vi performs 3 functions 1 It returns a list of available conductance modules Because the order of modules in this list has to reflect the order in which the conductance module VIs are implemented in V dependent Conductances vi assembling the list involves Create Plugin List vi several steps The process starts with letting Create Plugin List vi search the library Embedded llb for all VIs with type specifier unique type specifier WI ref for conductance JE ea module VIs Page 56 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide Create Plugin List vi uses Open VI reference and the provided type specifier to open every VI in Embedded llb Open VI reference will return an error with every VI of a different type 1 e with every VI that has a different connector pane Before the list of conductance modules 1s sorted into the correct order the settings for each conductance are retrieved from the configuration file Embedded cfg For each conductance module the content of the string control VI Label is obtain
15. application reference is closed The first type specifier VI Refnum control is set to the VI server class Strictly typed VI This VI server class can not invoke the method Make Current Values Default Therefore the second specifier VI Refnum control is set to the more general VI server class VI Page 17 of 88 Target application reference Initialize 4 1 6 DAQ Board Configuration This case is invoked by the menu item File gt Preferences gt DAQ Board Configuration when the user wants to change the settings for the analog input or analog output channels used This case operates analogous to the previously outlined case PXI Target using Embedded llb AnalogInOutConfig vi section 4 1 5 PXI Target 4 1 7 Selection Modified This case is executed after using settings virtualG s Templates camp one of the two front panel controls us A Available templates Selected templates for selecting or deselecting a 0_5K GTY 20K GTY h template Because the two controls 10 GTY 1_5K GTY are associated with the same event Aa 1PRIMARY GTY 1RC_PRIM GTY case of the Event Structure in the UE 2_10M5 GTY default case Check Controls see 2 12MS GTY 2 _14MS5 GTY section 4 1 3 and because they 2 15MS GTY 2 _16M5 GTY LT have opposing effects it is sufficient to query only one SelectTemplate of the two E controls in the Selection Modified case
16. are received the first TCP Read reads 4 bytes The Type Cast function 1s used to convert the string output of TCP Read into a long integer I 32 This number gives the number of bytes to read with the second TCP Read The string output of the second TCP Read is Type Cast into a 1 D array of single precision numbers SGL Because each experiment module VI sends two blocks of data with identical structure see section 4 1 13 Process for details the output of the third TCP Read is actually not needed because the output of the first TCP Read is used again to set the number of bytes to read for the last TCP Read The output of the last TCP Read 1s also converted to a 1 D array of SGLs and both arrays are combined to a 2 D array and temporarily stored in the hidden indicator Waveform Graph Finally the small Case Structure directs G clamp vi to the case Process in which the received data will be processed and analyzed Page 23 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide fo ne m ii E read data read data string size 1000 q E 4 1 12 Abort O Uses the TCP connection and TCP Write to send the TEP connection ID running experiment module VI a Boolean TRUE Type ras s Cast to a string of 1 byte causing it to abort the ongoing data acquisition This works only with experiment module VIs that perform a series of repetitive data acquisitions 1 e iterations as the
17. below which can also be found on NIs website or contact me Real Time FIFO for Deterministic Data Transfer Between VIs In LabVIEW Real Time RT applications you may need to transfer data to or from a VI set to time critical priority time critical VI This data can be transferred to or from a non deterministic system such as over the network to another computer or to the hard drive Typically the data is first transferred to or from a VI set to normal priority or a priority lower than time critical which we will call the Communication Loop Non deterministic operations can then be performed in the Communication Loop without harming the real time performance of the Time critical Loop The Communication Loop can then communicate with an external application over the network or perform File I O Figure 1 A common real time application structure Table of Contents o Communicating Data Between VIs Page 71 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide Using RT FIFO Creating an RT FIFO Opening a reference to an existing RT FIFO Writing when full or reading when empty Communicating Data Between VIs There are three methods to communicate between VIs global variables functional globals a VI that acts like a global variable and a RT FIFO FIFO stands for First In First Out Global variables are a lossy form of communication since there can be many writes to the global variable before a read is ever per
18. custom VIs to subroutine allows higher feedback loop rates than setting them to another level which would be overridden by the time critical setting of the calling VI As far as the possible execution systems are concerned in my opinion Application Note 144 doesn t provide any useful information at all and again one is forced to simply experiment with different settings 7 Application Note 144 is available from NIs website or installed as Lab VIE W manuals mltithrd pdf Page 44 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 7 Other experiment modules 7 1 Gsyn Threshold Gsyn Threshold vi is essentially a clone of IV Relation vi The only difference is that the number of data points per data acquisition iteration which is required to create the FIFO Result Data Queue is not derived from the variant DAQ Control Values but from the variant Template Template is converted to a string that gives the name of the template file to be used and the file is opened and read with read gsyn vi Required parameters as well as the template itself are transferred to Gsyn Threshold Sub vi via the RT FIFOs Control Values and Result Data Queue 7 1 1 read gsyn vi read gsyn vi first opens the template file for reading only and then determines the length of the file in bytes by calling EOF which returns the offset of end of file The byte length of the file 1s divided by 4 as t
19. cycle time Disabled sweep duration Disab sample rate Disable total number Disable Controls Page Enabled Rleak Period visible amini Gmax2 Wisib aminti Caption Tex Gmaxf2 Caption Te Show traces Visible Threshold visible 5 therefore array index 4 Its content should be grayed out indicating that it is not yet set and that the array does not extend that far Change the constants in the element to the desired values Even if the values are already correct change at least one value and set it back in order to activate the element thus effectively adding it to the array Note that the cluster element Controls Page Enabled State Page 66 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide is itself a 1 D array and you have to scroll through that array to see and set the appropriate enabled state for each page of the Controls control In the Enable Disable Controls case also add a new element to the 1 D arrays of strings that determine which template files will be available on the Template page of the Controls control Available templates Ei tDisabledItems If the new experiment module a does not use templates at all set the new string element to a Space character b does use templates of type gty set the new string element to GTY c does use templates of type gtl gt2 set the new string element to GTI Page 67 of 88 Kullmann and Horn 2004b
20. file names for the data file saved on the PXI controller and the host computer the ending time coded as number of seconds since midnight of the trace acquisition as determined by the PXI controller is To instruct Synaptic Gain vi to save the traces to file and or transmit the traces for display to G clamp vi the two Booleans Save data and Show traces are assembled into an array and after flattening to string sent with the TCP Write function used on both computers The missing day of month information is obtained with a Get Date Time In Seconds and a Format Date Time String Trace transmission With each iteration of the outer For Loop one of the two traces is received via the TCP connection Transmission of the traces is broken into smaller segments thus allowing the user to monitor progress via the Status Page 29 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide indicator The initial TCP Read in the outer For Loop serves to receive information about the number of segments to expect next and to set the count terminal of the inner For Loop The inner For Loop works in the same way as data transmission in the New Data case The first TCP Read receives information about the number of bytes to read with the second TCP Read 1 e the segment length Each received segment is immediately unflattened from string and appended to a 1 D array of SGLs which uses a shift register to ma
21. first opens a file for reading only and reads the first 19 SGLs 1 e the header into a 1 D array From the header array it extracts the mean presynaptic activity fpre Hz index 10 the length of the template ms index 11 the time to wait after execution sec before starting another experiment index 13 the sample interval ms index 0 and the of secondary synapses index 9 Because the first and the last of these parameters have different meanings depending on the template file type the type is determined by reversing the file name and comparing 28 For some unknown reason it was impossible to read very long template files and write very long data files in a single file read or file write operation This problem could be overcome by repetitive reading writing 1 e breaking the data into chunks 5120 is an integer multiple of 128 128 data points SGLs are 512 bytes which 1s the hard disk sector size in LabVIEW RT on a PXI controller Thus 5120 was chosen to optimize file transfer rates see section 11 2 File I O in LabVIEW RT Page 48 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide the first string element with 2 for gt2 For a pair of a gtl and gt2 file the fpre values correctly reflect the mean frequency of events in the gtl file and of events in the gt2 file and are summed up in the For Loop The number of secondaries can be ignored in the For Loop iteration reading the gtl file as th
22. for a period equal to 1 scan rate allowing other lower priority processes including the user interface TCP IP communication file I O etc to run Furthermore only the time critical priority setting ensures a 1 to 1 correlation between your control loop and scanclock signal If set to normal priority for instance Al SingleScan will be allowed to read from the onboard FIFO when an active scanclock edge arrives OR when there is a backlog of data in the FIFO You can verify that this sleeping functionality is enabled by looking for the following entry in your NI RT INI file associated with the target on which you are executing code NI DAQ Page 76 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide UseSleeping TimedNonBuffered TRUE This entry is present by default for all networked RT Series PXI Controller targets Networked RT Series PXI Controller s NI RT INI files can be found in C NI RT INI of the target s hard drive The Al Single Scan sleep mode is not turned on by default for the 7030 family RT Series DAQ devices The 7030 product family s NI RT INI file can be found in your LabVIEW RT Resource folder With NI DAQ 6 9 1 you can also use a counter on an E Series board DAQ STC counters only to control your loop rates Report Date 01 15 2001 Last Updated 11 04 2003 Document ID 25E9K94U Hardware Timed Loops Using AI SingleScan Al SingleScan VI one of the Advanced Analog Input VIs is often used in single point
23. new parameters requiring additional front panel controls on G clamp vi will be discussed in section 9 3 9 1 Creating the module The easiest way to create a new experiment module is to duplicate an existing module and modify it Because path information to sub VIs 1s stored with the calling VI and the LabVIEW RT run time engine on the PXI controller 1s not able to find a sub VI in the library Embedded llb if the path does not explicitly point into the library We strongly recommend the following procedure Copy Embedded llb from the PXI controller to a directory c ni rt g clamp on your host computer 1 e paths to Embedded llb are identical on the host computer and on the PXI controller You are also going to need a directory c ni rt g clamp gModules on the host computer that contains the conductance module VIs gNa vi eKdr vi implemented in Embedded lib V dependent conductances vi Temporarily remove or rename all other copies of Embedded llb on the host computer If you rename them rename the extension llb because that is what identifies 1t to LabVIEW as a LabVIEW library The reason for making all other Embedded llb copies on the host computer invisible to LabVIEW is to prevent any accidental loading by the new experiment module VI of one of its a sub VIs from one of these Embedded llb copies that have a directory path different than c ni rt g clamp Open the experiment module VI you want to use as a template fr
24. of a repetition of the sequence voltage change command increment decrement command optional and wait command Thus the 1 Match Pattern determines the voltage command type const step change or ramp If the 2 Match Pattern finds an increment or decrement command next the numerical value of the 1 Fract Exp String To Number is incremented decremented by the numerical value of the 2 Fract Exp String To Number multiplied with the iteration 1 terminal of the large For Loop The next command is supposed to be a wait command thus the 3 Match Pattern is used only to interpret the next numerical value which specifies the duration of the new command voltage Having obtained all necessary information for this section of the script a Replace Array Subset updates the zero values of the corresponding part of the 2 D command array to the intended voltage values 33 We simply haven t bothered to figure out the exact cause Page 61 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide The large For Loop stops once the 1 Match Pattern finds an end command or if the offset past match output returns 1 indicating that no regular expressions satisfying the criteria for a match have been found 8 5 TargetList VI TargetList vi contains a 1 D array of cluster with each cluster containing necessary data about one available PXI controller Execution of TargetList vi consists of waiting for user input to either extend t
25. our rationale for choosing certain programming structures over possible alternatives Some of the decisions we made in designing G clamp simply reflect generally principles of efficient LabVIEW programming and will thus be familiar to experienced LabVIEW programmers Hopefully these sections will also be helpful to those G clamp users who are less experienced in LabVIEW programming yet wish to understand how the program works In addition to describing aspects of G clamp that adhere to standard LabVIEW conventions this manual also stresses programming techniques that are specific to real time applications using LabVIEW RT In particular we wanted to outline the concepts that went into creating a dynamic clamp program that not only does the job but that gets maximum performance out of the hardware Having made such a bold claim we do not wish to imply that G clamp lacks room for improvement Quite the contrary we believe that through continuing use in electrophysiology experiments we and others will discover limitations in the present program and ways to further enhance performance In this spirit we encourage comments and suggestions for improvements in the program and in the documentation that we have written 2 Future direction of G clamp development Since its beginning in the spring of 2001 the G clamp project has evolved through numerous changes Although the present version 1 2 is fully functional the program remains in a continui
26. to DBLs before a trace 1s transmitted to the host computer has been E deleted The same was done in f Bo_ l o 00 Waveform Graph Embedded IIb Synaptic Gain vi E Bal a with the two 4 element 1 D arrays transmitted to the host after execution of the template In G clamp lIb G clamp vi this necessitated the following changes In the New read data Data case the data format of the 1 D array PSTL cons tan t an d O f the ee A E eared eed eae 0 Saeed edhe Seeds 0 Ie tad a e e dd z indicator Waveform En Graph was also changed f to SGL In the Process case the inputs to all Build Waveform functions were changed to DBLs while the format of the controls indicators A D rate RT Loop Info G scaling G s fpre and Gain was changed to SGLs G clamp lIb G clamp vi and Embedded llbiSynaptic Gain vi Conversion of the two Boolean controls Save data and Show traces into word integers I 16 before they are TCPed to Synaptic Gain vi in the Process case of G clamp vi has been removed Accordingly the TCP transmission is interpreted in Synaptic Gain vi as an array of Booleans and not any more as an array of I 16 Embedded llb Synaptic Gain vi The sequence of two Array Subsets in each of the two For Loops of the Case Structure saving the acquired traces has been reduced to one Array Subset G clamp IIb G clamp vi In the Plot all case in the first Wavefor
27. 4 Overwrite Output If you perform a read when the RT FIFO is empty then the empty output will be TRUE empt s Figure 5 Empty Output Real Time FIFO Example Page 73 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide It is suggested to place RTFIFO LLB into a sub folder of the user lib folder of your LabVIEW system directory This will make the VIs accessible via the User Libraries button in the Functions Palette Placing NBFIFO DLL into the same directory ensures that LabVIEW will find the DLL automatically when needed 10 2 Read Time Stamp Counter rdtse from National Instruments website Measuring the Determinism of Real Time Applications 5 1 2 S Print this Page This example demonstrates a method of measuring the determinism or jitter of an application using the Read Time Stamp Counter RDTSC assembly instruction for Pentium class processors This method of timing can resolve timing measurements at the frequency of your Pentium class processor In this example a top level VI that is set to NORMAL PRIORITY calls a subVI set to TIME CRITICAL PRIORITY HIGHEST The subVI has been instrumented with the RDTSC assembly call to read the Time Stamp Counter register off the Pentium class processor every loop iteration In order to avoid memory allocations the array holding the time stamps is pre allocated outside the For loop Each subsequently measured time is then placed into the array using the Replace Ar
28. Controls 7 If the selected menu item does not reflect a change in experiment module the menu item tag is fed into the queue causing the case with the same name as the menu item to be executed later zH ItemPath 3 SelectTemplate DeselectTemplate feeds the string Selection Modified into the queue whenever a template gets selected or de selected on the Templates page 4 start stop reacts to the Start F12 button and provides the queue either with a string causing the start of an experiment or its abortion 5 IV Relation reacts to mouse up events in the graph on the IV Relation page A mouse up event in this graph is dragging one of the cursors to a new position The only action of this case of the Event Structure is to calculate the leak resistance 8 Custom run time menus can contain user defined menu items and standard LabVIEW menu items application items Application items used in a custom run time menu require no additional programming as they behave in the same way as in the standard LabVIEW menu Page 14 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide This is done by using the property Cursor Position Cursor X and Cursor Position Cursor Y to obtain the cursor coordinates and thus the endpoints of the line for which the slope 1 e leak resistance 1s calculated IY Relation E BE 6 The Timeout case does not effect anyth
29. DeselectTemplate The control Available templates 1s a Listbox control whose output is a 1 D array of long integers I 32 with each number reflecting the index of the currently selected item s The indicator Selected templates is a Table indicator whose output is a 2 D array of strings only the first column of the table 1s visible Selecting a template The Value property of Available Templates is used to index the 1 D array of strings which is the control s property Item Names 1 The resulting 1 D array is appended concatenated to a 1 D array containing the templates that had been selected earlier and that are visible in the indicator Kullmann and Horn 2004b G clamp Programmer s Guide Selected templates 2 This 1 D array has been obtained by using Reshape Array to convert the 2 D array reflecting the Value property of the indicator Selected templates which contains elements only along one dimension 1 e the first column into a 1 D array 3 Lastly the concatenated 1 D array is converted back into a 2 D array using a Build Array to update the Value property of Selected templates 4 EE b E Selected templates De selecting a template The property Selection Start of the indicator Selected templates contains the row and column index of the beginning of the data selection The row index 1s obtained with an Unbundle and used at the row
30. Event Structure by executing the appropriate event case s If no event occurred the Event Structure waits for a certain time before timing out and letting G clamp vi execution proceed Thus the architecture of G clamp vi as a queue driven state machine ensures that G clamp vi execution performs only required actions without wasting processor time on executing currently unnecessary functions Use of the Event Structure guarantees that no user interaction goes undetected and is dealt with in the correct order while in the absence of a user interaction waiting of the Event Structure until it times out or an event occurs keeps G clamp vi idle and thus the host computer s CPU free to perform other tasks The following sections will provide a detailed look at G clamp vi by systematically going through individual cases of the state machine 4 1 G clamp start and program initialization Code execution starts with creating the queue inserting the string Initialize into it and with initializing several shift registers that are used to carry the values of several variables from one iteration to the next of the large outer While Loop The queue VIs used are LabVIEW 6 0 style which allow only strings to be used as queue elements In LabVIEW 6 1 these VIs have been replaced with queue VIs that allow any data type to be used Page 8 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 4 1 1 Initialize An Open VI Referenc
31. For next revision This can be fixed with an Invoke Method Set Control Value in the Initialize case of G clamp vi right before Run VP is invoked Page 59 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 8 4 ScriptAnalyzer VI This VI is part of Embedded llb It analyzes the voltage command script in the V clamp module and builds the command signal which is then output to the recording amplifier Interpretation of the script requires identification of the commands and the numerical values that follow almost all commands As the whole script is a single string the string functions Match Pattern and Fract Exp String To Number are used in a repetitive manner Match Pattern finds the first number in the string by searching for a regular expression defining a number see Description of reg expression in Figure 8 1 The string is then split into a substring with all characters before the number command a Space a substring with all characters making up the number and a substring with everything after the number remainder of the script The string making up the number is then converted to a numerical value with Fract Exp String To Number Dor 1 mio tch O or i Figure 8 1 eth E a The first time this mechanism is employed ScriptAnalyzer VI expects the for command Thus obtaining the substring with all characters before the number is actually unnecessary and the corresponding output of Matc
32. G clamp Programmers Guide version 1 2 Paul H M Kullmann and John P Horn Department of Neurobiology and Center for the Neural Basis of Cognition University of Pittsburgh School of Medicine E 1440 Biomedical Science Tower Pittsburgh PA 15261 http www neurobio pitt edu To download this document and the G clamp program go to http hornlab neurobio pitt edu Contact Information Dr Paul H M Kullmann Phone 412 648 9291 pkullman pitt edu Dr John P Horn Phone 412 648 9429 jph pitt edu Grant Support This document and the G clamp software that it describes were both developed at the University of Pittsburgh with support from National Institutes of Health grant RO1 NS21065 Copyright Information These materials are freely available for non commercial research and educational purposes The authors reserve the copyright and request that others using this material acknowledge its origin Those wishing to publish any of this material or to develop commercial applications must first contact the authors First Edition 2003 Revised October 1 2004 Copyright 2004 Kullmann and Horn 2004b G clamp Programmer s Guide Table of Contents Whoshould read this tude susscteiih seri aia ta cu seed a daha cu eau att 4 Future direction of G clamp development ooooooonnncnnnnnnnnnononocccnnnnnnnnnnnanoccnnnnnnnnnnnnos 4 Overview of G clamp program architecture oooonnnnnccnccnnnnnnccnononnnnnnnnnnnnnnnn
33. GLs would be done after reception by G clamp vi With this scheme memory requirement for the RT FIFO and therefore RAM usage on the PXI controller could be much reduced provided that a the communication loop can read the queue and transmit the data fast enough compared to the speed at which the RT feedback loop writes to the queue and b the sleep modus for AI SingleScan vi is set to TRUE in ni rt ini see section 11 1 AI SingleScan s sleep mode Following the G clamp installation instructions given in the G clamp User Manual the sleep modus should be set to FALSE to achieve faster maximum RT feedback loop rates For next revision 10 is unnecessary Provide a constant of value 1 as input 6 For next revision No EOC Error vi in front of TCP Close Connection is unnecessary U For next revision The start of IV Relation Sub vi should be made dependent on successfully establishing the TCP connection and establishing Result Data Queue which would make it possible to set the return existing input of RTFIFOCreate DBLA vi in IV Relation Sub vi to TRUE instead of the default FALSE Page 34 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 5 1 Operation of the communication loop The first process in the loop is to wait up to 250 ms for a TCP transmission from G clamp vi of a single byte which 1s then Type Cast to a Boolean A Boolean TRUE 1s the signal for IV Relation vi that the user wants to stop the experiment and gave the A
34. IEW RT 6i The 7030 product family s NI RT INI file can be found in your LabVIEW RT Resource folder 11 2 File I O in LabVIEW RT From National Instruments knowledge base Optimizing File I O in LabVIEW and LabVIEW RT This document will explain how file I O works and show how to optimize file I O performance in various operating systems including LabVIEW RT OS Table of Contents How does file I O work What is caching and how does it affect file 1 0 How can optimize file l O in LabVIEW How is LabVIEW RT different How can optimize file I O in LabVIEW RT How does file I O work Every operating system OS is responsible for implementing a file structure However the basic concepts are the same for all operating systems We will begin by looking at the structure of a disk which is the physical medium on which data is stored The disk generally consists of several platters It is easy to think of a disk as a record player To access the data on the disk two read write heads attached to a single arm are moved to the correct location The platters are divided into equal sized tracks A track is made up of sectors These sectors are the unit of data transfer So while users and applications think in terms of writing records the operating system breaks these down into writable sectors which it then writes one at a time When the disk drive is operating it is rotating at a constant speed To read or write a sector of
35. Muto Dispose Ref Type Descriptor Type Descriptor e ct LLL ETA Virtual G s Available templates Virtual G s O ee Pale ue The strings returned by the method Get Control Value are unflattened Some further processing 1s required before the names of the available template files can be made visible to the user by updating the property ItemNames of the Listbox control Available templates Because the control Virtual G s of List Templates vi is an exact copy of the control on the Virtual G s page of the G clamp vi front panel the output of Unflatten From String can be used directly to update the Value property of the that control Again for later use in other cases the information about the virtual conductances is bundled into the corresponding cluster element of the large cluster that is passed from one iteration of the outer While Loop to the next via the top shift register While steps to 3 are in progress G clamp vi prompts the user to specify the directory on the host computer used for saving data files Page 10 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide new or existing dir Select data directory on host computer This information is also bundled into the corresponding cluster element of the large cluster that is passed from one iteration of the outer While Loop to the next via the top shift register An Enable Disable Controls and
36. ader length of the template file has been removed LoadTemplates vi The input HeaderLength Bytes has been removed and the shift register feeding into the pos offset input of Read File is now initialized with the offset output of the Read File used to get the template header o In G clamp IbiG clamp vi In the Enable Disable Controls case enabling disabling of gtm files in the Available templates control has been removed In the Selection Modified case the second Case Structure changing display properties of the controls Gmin l and Gmax 2 has been removed Embedded llb has been stripped of all VIs that are not used by G clamp This was done by renaming Embedded llb opening all VIs called via VI server by G clamp vi from the renamed library and saving them with File gt Save with Options gt Save entire hierarchy into a newly created library Embedded llb Because this saves also the conductance module VIs gNa vi gKdr vi into the library V dependent Conductances vi was opened and all its implemented conductance module VIs replaced with the same VIs from the directory c n1 rt g Page 85 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide clamp gModules Finally the conductance module Vis were deleted from Embedded lib Embedded lIb IV Relation vi ES a False ne Embedded llb Gsyn Threshold vi E and Embedded IlbWV clamp vi The conversion from SGLs
37. as the number of elements in the RT FIFO increased Determinism or real time behavior of time critical VIs would be harmed if this dynamic memory allocation occurred inside of the time critical VI To specify the size of the RT FIFO wire the desired size to the size input terminal of the RTFIFOCreate VI In Figure 4 an RT FIFO of 20 elements is created Figure 4 Specifying the RT FIFO Size Opening a reference to an existing RT FIFO To open a reference to an existing RT FIFO use the RTFIFOCreate VI with the name of the RT FIFO wired to the name terminal and a TRUE wired to the return existing terminal as shown in Figure 3 Figure 3 Opening a Reference to an Existing RT FIFO Writing when full or reading when empty If you perform a write when the RT FIFO is full the oldest element is overwritten and the overwrite output will be TRUE To avoid overwriting elements you need to either make sure that the reader will always read elements from the RT FIFO faster than they are written or you need to ensure that the RT FIFO is large enough to contain the elements that are written to it while the reader is unable to read You also need to make sure that the reader has the ability to catch up to the writer In other words the reader needs to be able to read points from the RT FIFO faster than the writer on the average and the RT FIFO needs to be large enough to store elements while the reader is busy ETETEN overwrite n Figure
38. ask IDs for the analog input and analog output operations used in the real time feedback loop module G clamp DQA vi These task IDs are re used with each data acquisition iteration of the While Loop as the associated operations are cleared by G clamp DQA vi at the end of each data acquisition iteration From the variants AI Cluster and AO Cluster DAQ Hardware Settings vi also provides the recording amplifier specific scale factors for the analog input and output signals to Build AO waveform vi and G clamp DQA vi S To use the variant control AI Cluster to get the info about the processor speed from G clamp vi to the experiment module VI is not very logical It s even confusing as it is a hidden element of the cluster control AI Cluster Page 37 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 3 Build AO waveform vi generates a scaled analog output waveform that will be added to any output signal calculated by the real time feedback module G clamp DQA vi due to virtual conductances Thus the waveform has as many data points as will be acquired by analog input and send out by analog output The loop iteration count provided by the iteration terminal 1 of the While Loop 1s used by Build AO waveform vi to increment the current step 4 The RT feedback loop module G clamp DQA vi acquires one data point at a time calculates the new command signal for the recording amplifier and outputs it The ope
39. ber of action potentials elicited by the executed template This is done with Peak Detector PtByPt vi While the point by point analysis VIs are designed to be used in a E 51 control loop by processing continuous data streams one point at a time they require some overhead ultimately slowing Ear down a control loop that 1s supposed to run as fast as possible Note that the accuracy of Peak Detector PtByPt vi depends on the width input which is set to a constant Thus if width is too narrow for the width of an action potential at a given sampling rate Peak Detector PtByPt vi can miss peaks Page 50 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide After Synaptic Gain Sub vi has finished the results are communicated to G clamp vi via the TCP connection l Mean presynaptic frequency fpre Hz output from LoadTemplates vi synaptic gain APs output of Synaptic Gain Sub vi divided by total number of presynaptic events ending time of the experiment as seconds since 12 00 AM and actual sample rate elements 0 and 1 of Output Array from Synaptic Gain Sub vi are assembled in that order into a 1 D array of 4 elements converted to a string the length of this string also converted to a string concatenated in front of the string and sent via a TCP Write to G clamp vi voltage trace a FS EE 2 Inthe same way the RT Info output of Synaptic Gain S
40. bort command see section 4 1 12 Abort Type Cast returns a FALSE if TCP Read receives nothing and times out An abort signal is transmitted to IV Relation Sub vi via the RT FIFO Control Values The stop element of the cluster Controls is set to 1 and after Cluster To Array added to the RT FIFO queue The smaller While Loop within the communication loop performs a read on the RT FIFO Result Data Queue If the queue has not been empty and 1f no Abort command was given the removed queue element trace is Type Cast to a string the string length determined and after conversion to a string added in front of the trace string and via a TCP Write sent to G clamp vi For each trace transmitted a counter 1s incremented to stop the communication loop after all traces have been sent to the host computer Note that execution of the communication loop is preempted by the real time feedback loop which has the highest execution priority to maintain determinism Thus transfer of data traces 1s usually limited to the period in between two data acquisitions iterations 5 2 IV Relation Sub vi The Sub vi of an experiment module VI 1 sets up the RT FIFO queues Control Values and Result Data Queue 2 sets up the data acquisition board for the intended analog input and output operations 3 prepares the output signal to the recording amplifier by interpreting the user settings with Build AO waveform vi or reading a templa
41. by outputting a 0 voltage This is in case that the output registers for both channels took on some arbitrary values as can happen after starting the PXI controller It also performs a short data acquisition on analog input channels 0 and 1 which apparently is required to initialize the analog input hardware after the PXI controller has been started This function has a serious flaw The control device 1 which provides AI Config vi and AO Config vi with the device number of the installed DAQ board is not updated at all Thus correct functioning of the reset process depends on having set the default value of the control device 1 to the correct number for a given PXI controller 83 SaveConfig VI virtual G s This VI is part of Embedded llb It E o dd Meg Fast Sodium g 300 00 conductances to the configuration _ controller Note that Write Key vi a J40 00 y OT eak 2 Cabinn E A i 4 00 i E writes the settings for the virtual does not actually write to file but only predisposes a key for writing To achieve the actual write co ni rtlo clamplembedded c o operation the write configuration file input of Close Config Data vi has to be set to TRUE z MN El 31 We observed that without this analog input operation during G clamp initialization the first real data acquisition performed by G clamp as an experiment will result in bogus values 2
42. caleFactorUsed Kullmann and Horn 2004b G clamp Programmer s Guide hard wired into the program as a constant Note that an Array Subset is used to eliminate the first 200 data points of the trace from the analysis This eliminates any 0 crossings that can occur as a consequence of initially arbitrary state variables when virtual voltage dependent conductances are used especially when used together with a passive RC circuit which has no sub zero potential initially Depending on the outcome of the comparison the content of either the Gmin shift register or of the Gmax shift register is replaced with the scaling factor used for the previous data acquisition iteration Note also that the While Loop contains Build AO waveform vi which is used in IV Relation Sub vi to generate the DC current command This allows execution of a template file in combination with a constant current injection 7 2 Synaptic Gain The architecture of Synaptic Gain vi differs from the other experiment module VIs Synaptic Gain vi executes a potentially very long template file a single time Thus no loop structure is required to repetitively transmit acquired data to the host and no RT FIFO is used to transfer the acquired traces voltage and current trace from Synaptic Gain Sub vi to Synaptic Gain vi In addition because transfer of very long traces to the host computer can take a long time it is optional This necessitates a function to save acqui
43. cific settings required for execution of the experiment module This process will be explained in more detail below It next starts the experiment module VI by invoking the method Run VI with the parameter Wait until done set to FALSE This allows code execution of G clamp vi to proceed without waiting for the experiment module VI to finish Lastly it uses Open TCP Connection to establish a TCP connection with the experiment module VI that will serve to transfer the acquired data from the experiment module VI on the PXI controller to G clamp vi on the host computer If all these actions occurred without an error 1 e the status variable of the error cluster is FALSE a string Send Control Values is fed into the queue Because no case Send Control Values exits the default case Check Controls will l This is the reason why after a re boot of the PXI controller G clamp vi also has to be re started Re booting the PXI controller makes the application reference invalid and G clamp vi has to obtain a new one 2 This is a leftover from a former case Send Control Data Any string including an empty string could be used here to force execution of the default case Check Controls next Page 20 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide execute next With the variable DAQ in process now TRUE Not FALSE the queue will be provided in Send Control Values with a string di
44. clamp vi In the case of the Process case processing data from the Synaptic Gain module decoding of the trace acquisition time has been changed The old version used the Format Date Time String function This function assumes that the input seconds now is relative to 12 00 a m January 1 1904 Universal time while in fact the number of seconds provided by SecondsToday vi in Synaptic Gain Sub vi is relative to 12 00 a m of the current day G clamp IIb G clamp vi In the Stop case using the Property Node Execution State to determine when to close the reference to the experiment module VI is not necessary and has been removed by deleting the whole While Loop G clamp IIb G clamp vi In the Stop case the experiment module specific condition for adding a string Start ExpModule Stepl to the queue is now determined by comparing the variable Exp Type with a 1 D array containing an element for each experiment module for which the condition ought to be TRUE Embedded Ilb Gysn Threshold Sub vi Instead of calculating again the correct values for the elements in array and size inputs of RTFIFOCreate SGLA vi to initialize Result Data Queue the return existing input was set to TRUE Now Gysn Threshold Sub vi simply opens a reference to Result Data Queue as created earlier in Gysn Threshold vi The same was done with RTFIFOCreate SGLA vi that initializes the RT FIFO Control Values
45. corresponding TCP Read in the experiment module VI is located in the While Loop that runs parallel to the RT feedback loop module in these VIs and that sends data to G clamp vi in between iterations 1 It uses Flush Queue vi to empty the queue and then inserts so the string Stop 2 It clears the indicator Selected templates by setting its property Value to an empty 2 D array HO rmm S Because of the unwired timeout input TCP Write times out after the default 25 000 ms This means that in situations in which the While Loop in the experiment module VI needs more than 25 000 ms for an iteration the Abort command goes unnoticed Page 24 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 4 1 13 Process This case processes and displays the data sent by the experiment module VI in a Case Structure which has one case for each experiment module with code intensive processing split into different frames of Sequence Structures The processing logic of the data 1s the same in each experiment module case and will first be illustrated using the IV Relation case Second experiment module specific differences will be explained l General outline of data processing The data to be processed are read out from the Value property of the hidden indicator Waveform Graph As described in section 4 1 11 New Data Waveform Graph contains two rows of data assembled from tw
46. cts data from the onboard FIFO buffer which has begun to store data In the Windows operating system we can ensure that Al SingleScan will capture all data without any overwrite errors if the loop rate is faster than the hardware scan rate However if the control loop rate is slower than the hardware scan rate we will eventually overwrite unread data in the FIFO In the real time OS the hardware scan rate controls the loop rate Al SingleScan acts like a wait statement in the loop until the next active edge of the scanclock wakes Al SingleScan When Al SingleScan wakes up it executes as normal collecting one scan of data from the onboard FIFO When Al SingleScan is called in the next loop iteration it sleeps until the next active edge of the scanclock wakes it up again Thus Al SingleScan synchronizes your control loop to the hardware scanclock You can monitor the output parameter of Al Singlescan called scans remaining to determine whether the overhead in the loop is preventing Al SingleScan from capturing all data i e keeping up with the scanclock rate In addition to increasing the maximum achievable control loop rate past 1 kHz Al SingleScan s sleep mode or sleep pathway benefits multithreaded applications A control loop running at time critical priority will starve other low priority threads if there is no delay or sleep mode built into the loop Al SingleScan s sleep mode ensures that your time critical code relinquishes the CPU
47. d into the user interface G clamp vi At present every experiment module is hard wired into G clamp vi and this requires making changes at several program locations into order to add a new module The revised program would simplify the process by implementing a plug in architecture At program start G clamp vi would scan the plug in directory for experiment modules and make them available for the user Thus would reduce to process of programming or modifying an experiment module VI to the simpler task of writing the module and placing it in a plug in directory Provide error debugging information from program components executing on the embedded computer during development of new experiment modules Page 5 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 3 Overview of G clamp program architecture G clamp v1 2 consists of 2 parts that are divided between the host and embedded computers 1 The library G clamp llb resides on the host computer G clamp llb contains G clamp vi which acts as the G clamp user interface G clamp vi 1s marked as a top level VI in G clamp llb and thus opens automatically when G clamp llb is opened The remaining files in G clamp llb which are either standard LabVIEW VIs or custom VIs all operate as sub VIs in G clamp vi 2 The library Embedded llb resides on the embedded computer Embedded llb contains the VIs that constitute the experiment modules the RT loop module and the conductance mod
48. d to be implemented twice once for the voltage trace and once for the current trace each followed by its own RTFIFOWrite SGLA vi which would need to be properly chained to preserve the correct alternating order of elements in the queue voltage trace current trace voltage trace current trace On the other hand the use of the For Loop auto indexed by the 2 D array makes it easy to add additional channels for transfer to the host computer Page 38 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 6 Finally once the last data acquisition iteration is complete and the While Loop stops AO Write One Update vi sets the analog output channel used to 0 This serves as a fail safe mechanism to prevent a last current command used in the While Loop and different from 0 to persist as command input to the recording amplifier 5 2 1 The RT feedback module G clamp DOA vi The task of this module is to read from an analog input channel the membrane potential of the cell under study calculate the new current value through the virtual conductance s and write the current command to an analog output channel This task is repeated in a While Loop for the length of the experiment at the rate specified O ea Before the loop starts executing three operations are performed 1 is subtracted from of data points This value compared with the current loop iteration count yields the stop condition for the Whi
49. data we must correctly position the heads at the beginning sector of the correct track The time required to move the head to the correct track is seek time The time for the disk to rotate until the starting sector is under the head is known is rotational delay The sum of these two numbers is known as access time The time to complete the read and write operation is known as the data transfer time What is caching and how does it affect file 1 0 In general a cache is a buffer that is used as an intermediate and faster data storage medium More specifically a disk cache is a buffer in main memory that maintains a local copy of disk sectors Accessing main memory is significantly faster than accessing the disk When an application needs to write to a sector on disk the operating system first checks to see if that sector is available on the cache If it is no access to the disk is required The data is written in main memory Some time later the contents of the cache will be written out to the disk If the sector is not found in the cache the sector will be brought in from the disk to the cache Caching is used to reduce the average access time by assuming that a sector that was written to once will likely be written to again some time later There are many different design implementations of this idea with various cache size implementations How can optimize file I O in LabVIEW Before we discuss optimization methods in LabVIEW we ne
50. ds since 12 00 AM into an intelligible string and combines it with a string giving the day of the aH gail month to produce the data file name It concatenates the name s of the template file s used into a string and checks whether the string length is an integer multiple of 4 If not it adds Spaces to fulfill this condition which obliterates any bit shifts when reading out the header of the file by reading everything from the beginning as an array of SGLs It creates the data file with New File writes a SGL giving the length of the string with the template file names the string itself and the a 1 D array of SGLs Page 52 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide supplied by Synaptic Gain vi which contains other header information It uses the offset output of the last Write File to get the current length of the file and if necessary it adds bytes I 8 to extend the file to a length of 512 bytes Having a header of 512 bytes means that subsequent writing of the trace data starts with a new disk sector and therefore in the most efficient way see section 11 2 File I O in LabVIEW RT Synaptic Gain vi next writes the traces to file first the voltage trace and then the current trace by breaking each trace into smaller chunks of 5120 data points or less for the last chunk Page 53 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 5 Onl
51. e Voltage and Current are re initialized in the Start ExpModule Step1 case with an empty array Calculation of the leak resistance is done in the IV Relation case of the Event Structure in the case Check Controls 1 e whenever the user moves the cursors in the xy graph Structure of the 1 D array of DBLs Waveform Graph o index 0 start time of the trace acquisition coded as seconds elapses since 12 00 AM Page 27 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide o index 1 reciprocal of the actual sample rate Hz of the analog input operation o Index 2 not used set to zero o index 3 6 RT loop performance information o index 7 n voltage and current trace respectively Gsyn Threshold The scaling factor used with the last received set of traces 1s fed into the numerical indicator G scaling and into the waveform chart Gsyn ThresholdChart History length of Gsyn ThresholdChart is set to 100 data points The 1 D array of DBLs G s serves as a buffer for the scaling factors before they get saved to file and is re initialized in the Start ExpModule Step1 case with an empty array Structure of the 1 D array of DBLs Waveform Graph o index 0 start time of the trace acquisition coded as seconds elapses since 12 00 AM o index 1 reciprocal of the actual sample rate Hz of the analog input Operation o index 2 factor used for scaling the conductance te
52. e Process case a new case has to be added to process the data acquired by the new experiment module As described above the easiest way to do this is to duplicate an existing case and modify it If the new experiment module requires analysis results either from analyzing a trace as with the IV Relation module or from extracting analysis results from the header as with the Gsyn Threshold and the Synaptic Gain module to be displayed a new page can be added to the front panel indicator Plots and indicators for the display of these experiment module specific results can be placed on that page 8 In the TRUE case of the Case 2 Menu Selection User Structure contained in case 2 Menu E ItemPath Selection User of the Event Structure in the Check Controls case the name of the new module has to be added to the string array constant Page 69 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 9 In G clamp llb GetDateFilename viadd an element to the string array to specify ol HMMS vb Yad eH oh 5 gth 2d HM 5 gaj C PadesHeen s new D i the 3 character file extension for the data files created by the new experiment module 9 3 New control parameters G clamp vi groups related parameters into a cluster In the Start ExpModule Step2 case clusters are converted to a variant and the method Set Control Value is repetitively invoked to transfer t
53. e next Case Structure executes Another cluster is added to the 1 D array of clusters containing the conductance n L i r gt hl E settings found in Embedded cfg with the cluster element VI Label set to the first element remaining in the 1 D array that triggered execution of the TRUE case Likewise the 1 D array of section names created in the previous For Loop 1s expanded by one element Lastly an entry for the new conductance module is made in Embedded cfg Note that this expansion of the 1 D array of clusters takes care of only one new conductance module If more than one new conductance module was created NI E Di only the first one found by Create Plugin List vi will show up on the front panel of G clamp vi irrespective of whether that one was actually the first new one implemented in V dependent Conductances vi Finally the 1 D array of clusters is re organized based on the order of elements in the 1 D array of section names It returns a list of available template files by searching the directory c n1 rt g clamp template on the PXI controller for files of type gty and gtl It does not check whether a corresponding gt2 file exists for each gtl file found The list Page 58 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide is available in the string indicator Available templates with file names separated by a Tab Constant 3 It resets both analog output channels
54. e VI Page 77 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide that Al SingleScan is in will sleep until the next active scan clock edge Since Data Aquisition is usually done at time critical priority the sleep mode of Al SingleScan is necessary to allow lower priority processes to run Without this sleep mode you would have to use Wait VI or Wait Until Next ms Multiple VI to make your VIs sleep to allow lower priority VIs to run but these Wait VIs only have resolution of 1 millisecond With this sleep mode Al SingleScan provides the right amount of sleep time automatically Preallocating arrays for Control Loops Since memory management harms determinism Al SingleScan has an input called data in Al SingleScan is a polymorphic VI meaning it can be configured for different data types The Single Point Waveform version is the most common version of this VI used in Real Time applications and is shown below This document will discuss the features of this VI specifically but the principles apply to the other versions as well acquisition state task ID out scaled data o error ouk data remaining task ID data in tempts opcode 0 no change error in no error time limit 1 auto calcul When data in is not wired a call is made to the LabVIEW Memory Manager to allocate an array for scaled data In order to prevent memory management an array of the same size as scaled data out is expected to be passed in T
55. e and Close File to determine the length of the template file has been replaced with File Directory Info 18 NOW Embedded llbiLoadTemplates vi After the template has been assembled a Replace Array Subset sets the value of the last template data point to 0 This brings the current command to 0 immediately at the end of the execution of the template As a consequence the AO Write One Update vi in Embedded llb Synaptic Gain Sub vi which performed this current command reset after some delay has been removed Page 88 of 88
56. e gtl file reflects activity of one Fpre synapse and 1 is added to the shift False h C SampleInterval ms emplateLength ms register During the second iteration of the For Loop the number of secondaries in the gt2 file is read out and added to the shift register Thus fpre Hz is obtained by dividing the sum of presynaptic mean frequencies by the sum of synapses Note that the outputs SampleInterval ms PostWait sec and TemplateLength ms reflect only the corresponding values found in the header of the last template file read from a series of template files The smaller For Loop within the large For Loop reads the template file in chunks of 5120 values except the last chunk which can be anything in between 1 and 5120 The For Loop uses a shift register to set the read start position pos offset input of Read File to the offset output of the previous file read operation For the first iteration of the For Loop the shift register is initialized with a constant of value 512 The chunk read is next multiplied with the scale factor for the template file and summed up with the row in the 2 D buffer array that it is going to replace This buffer 1s maintained with a shift register from one iteration of the large outer For Loop to the next Thus by continuously updating this buffer the memory requirement of reading and combining multiple template files is kept to the size of the fina
57. e provided with the path of G clamp vi is used to obtain a VI reference to G clamp vi This reference is subsequently used to invoke methods reinitialize all front panel controls to their defaults and to set properties front panel window title of G clamp vi For later use in other cases the G clamp vi VI reference is bundled into the corresponding cluster element of the large cluster that 1s passed from one iteration of the outer While Loop to the next via the top shift register 1 Reinitialize all controls findicators to default FE Reinitialize All To Default clamp Initializing 1 A VI reference to G clamp llb TargetList vi is obtained to invoke the method Get Control Value on the control PXI Target This control of TargetList vi contains all required information about the PXI controller last used The Get Control Value method returns a string which has to be converted into a meaningful data format This is done by providing the Unflatten From String function with a constant of the same data format as the control on which Get Control Value was invoked After the Invoke Node has executed the VI reference to TargetList vi is discarded with a Close LV Object Reference A Get Pxl feet tad target info Get Control value e Control Name p A TargetList vi Pal Target Type Descriptor DAG board device Processor speed MHz IP address Again for la
58. e queue contains only 1 element 2 As long as the feedback loop does not lag that much behind that the constant analog to digital conversions result in an overflow of the FIFO buffer In that case LabVIEW restarts the data acquisition board effectively canceling the analog input and output operations and thus probably get the While Loop stuck indefinitely Page 40 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide is read out with Index Array The element read out from DC command Vm Buffer corresponds to the next DC current command set up by Build AO waveform vi in IV Relation Sub vi and is summed up with the other currents through virtual conductances calculated in the feedback loop The element read out from Template Im Buffer is 0 when V clamp DQA vi is called with the IV Relation module When the Gsyn Threshold or the Synaptic Gain module uses V clamp DQA vi Template Im Buffer contains the conductance template read from file and already scaled by the respective Sub vi While the acquired current value is not used any further and simply stored in the buffer Template Im Buffer the acquired voltage value is used to calculate the driving force for the pre determined conductance read from a template file and fed into V dependent conductances vi to calculate the current through any active voltage dependent virtual conductances Although analog output is performed on only 1 channel AO Single Update vi requi
59. e settings can be used at the next start of G clamp vi This 1s done by invoking the method Set Control Value on the control Virtual G s of Embedded llb SaveConfig vi and then invoking the Run VI method with the parameter Wait until done set to TRUE After the VI reference to SaveConfig vi has been closed the reference to the LabVIEW RT Engine on the PXI controller is closed If the Exit command was given while an experiment was in progress the queue receives the string Abort followed by the string Done otherwise only the string Done 4 1 17 Done Closes the VI reference to itself and destroys the queue Besides selecting the Done case the output of Remove Queue Element vi also stops the outer While Loop thus terminating G clamp vi Page 32 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 5 An exemplar experiment module IV Relation VI IV Relation vi Gsyn Threshold vi and V clamp vi each perform a series of data acquisitions iterations and therefore these three VIs have essentially the same structure consisting of 2 processes that operate in parallel A communication loop transfers data to and receives commands from the host computer via a TCP connection and the real time feedback loop as the central component of the dynamic clamp From the wiring diagram of IV Relation vi the communication loop is immediately recognizable as the large While Loop The real time f
60. e specifics Thus the RT FIFO Result Data Queue is capable of storing the complete set of traces that will be acquired during the experiment The whole cluster obtained from converting the variant DAQ Control Values consists of 15 identical elements 1 e DBLs and can thus be converted with Cluster To Array into a 1 D array of DBLs This conversion retains the ordering of elements in the cluster and thus makes it possible to read out a specific element from the array with Index Array The 1 D array of DBLs is written to the RT FIFO Control Values which consists of 10 because 10 is the default value of the unwired size input of RTFIFOCreate DBLA vi gt 1 D arrays of 15 DBLs TCP Listen vi waits for up to 60 sec for G clamp vi see section 4 1 9 Start ExpModule Step2 to open a TCP connection on port 2055 After these initialization steps the communication loop and IV Relation Sub vi are ready to start executing 4 Tn theory the RT FIFO could be used to provide the communications loop with individual data points as they are acquired Instead of using a queue whose elements are 1 D arrays of SGL 1 e a complete trace the queue would consist of individual SGLs 1 e data points The RT feedback loop would write a new element to the queue during each loop cycle and the communication loop could transmit individual SGLs or assemble a few SGLs into a short TCP transmission Re assembling of the SGLs or short stretches of S
61. ecause we always write in 512 byte chunks you ll actually write 512 bytes both times This will significanlty degrade the peformance of the application Page 80 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 12 Revisions 01 16 2004 new revised G clamp v1 1 1 Embedded llb Timing Analysis vi Building of an array by indexing the output of a for loop has been replaced by using 1 an initialized array fed into a shift register of the for loop and 2 the replace array subset function This avoids using new blocks of memory that increase by array element with each iteration of the for loop As a consequence the longest GAI template that can now execute correctly on a PXI controller with 192 MB RAM increased from 25 4 MB to 30 5 MB replaced S gt Ta ter a TIHE with Embedded llb Gsyn Threshold Sub vi The constant feeding into the index input of the index array function that reads out the stop value for the iterations loop has been changed from 10 to 9 Now aborting an on going data acquisition works new Page 81 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide An analogous change has been made in Embedded Ilb IV Relation Sub vi and Embedded llb V clamp Sub vi Embedded llb Gsyn Threshold vi The true condition for the case structure in which data traces are written to the host computer via the TCP write function can now be achieved not only by an empty result da
62. ecute a sub VI that performs experiment specific operations e g loading a template from file or analyzing an acquired trace to adjust parameters for the next iteration and the dynamic clamp by calling the RT Loop module VI and use a dedicated TCP IP connection to send acquired traces to and receive user commands from the user interface VI While these two tasks are organized in parallel the high execution priority of the RT Loop module VI ensures that the dynamic clamp operation always takes precedence and thus communication with the user interface VI occurs only in between iterations or after the dynamic clamp experiment has finished Running the user interface on the host computer as a client for the experiment module VIs running on the embedded computer as opposed to downloading and executing everything on the embedded computer has advantages and disadvantages The main reason why this architecture was adopted was to be able to run dynamic clamp experiments uninterrupted for several minutes and thus to preserve as much memory as possible for templates used and traces acquired during such experiments The chosen architecture aids in this goal by delegating the memory and time consuming process of displaying traces to the host computer It also allows for other memory and time consuming processes like post experiment analysis to be delegated to the host computer The main disadvantage of this architecture is that when LabVIEW is tar
63. ed plo ry A Create Plugin List vi wa E te Fast Sodium _ a a a Get Control value Control Name Type Descriptor jas This string identifies a conductance in the front panel control Virtual G s of G clamp vi to the user and it serves here as the section name for that conductance s entries in Embedded cfg If an entry for a conductance exists in Embedded cfg the bundled settings for a conductance are added to a growing 1 D array of clusters A 1 D array of all the VI labels is passed to the next For Loop in which it is compared with a 1 D array obtained from Get Section Names vi and containing all section names in Embedded cfg A new 1 D array is built containing only those section names corresponding to conductance modules and in the same 30 Create Plugin List vi is a slightly modified version of an example VI downloaded from a National Instruments website illustrating how to program a plug in architecture in LabVIEW Page 57 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide order as in Embedded cfg i e in the same order as the conductance modules are supposed to be used in V dependent Conductances vi This still leaves open the possibility that a new conductance module has been found by Create Plugin List vi for which no entry in Embedded cfg yet exists In this case the depleted 1 D array of VI labels is not empty 1 e has a length of gt 0 and the TRUE case of th
64. ed to distinguish between two very different types of file I O operations Many applications require sequential access to a file where the file is read from or written to in order from the start of the Page 79 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide file to the end This type of application will benefit greatly from the caching mechanism since neighboring sectors will likely be in the cache Alternatively our application might require random access to the file That is we may need to access unrelated non neighboring sectors of a file This requires a very different way of thinking One thing to consider is that some file types are not easy to use for random access applications An ASCII file requires a varying number of bytes for each data element For example the number 756 requires 3 bytes of storage while the number 7 requires only 1 byte Therefore it is not possible to predict an element s location in the file To find the element you need you need to search the entire file This makes random access very difficult and very inefficient with ASCII files The solution is to use file types that are easier to search Binary files are a very good choice for random access applications since every element uses the same number of bytes in memory Since we know exactly where a particular element is we can easily index individual elements in a file How is LabVIEW RT different To maintain determinism LabVIEW RT does n
65. eedback loop is implemented as a sub VI G clamp DQA vi in IV Relation Sub vi in the Sequence Structure below the While Loop Data acquired by the real time feedback loop are transferred to the communication loop via the RT FIFO queue Result Data Queue while the RT FIFO queue Control Values serves to provide IV Relation Sub vi and the real time feedback loop with the essential experiment parameters for general information about RT FIFOs see section 10 1 TE Jl Control Vales a pos Bic Arm eat iy Chaster T i cll E Before IV Relation vi actually starts running the calling VI G clamp vi sets the variant controls DAQ Control Values Virtual G s AI Cluster and AO Cluster by invoking the method Set Control Value see section 4 1 9 Start ExpModule Step2 Once IV Relation vi starts executing the variant DAQ Control Values is converted to its original data format by providing the Variant To Data function with the cluster Page 33 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide Controls at its type input The parameter of iterations is multiplied by 2 for the voltage and the current trace and used to set up the number of elements in the RT FIFO Result Data Queue with each element consisting of a 1 D array of SGLs of length scan rate multiplied with sample duration plus header length see section 4 1 13 sub section 2 Experiment modul
66. es gt PXI Target when the user wants to change the PXI controller G clamp targets After a type specifier VI Refnum to Embedded llb TargetList vi has been obtained the property Front Panel Window Open of the VI is set to TRUE A Call By Reference Node is used to execute TargetList vi causing G clamp vi to wait until the user is finished selecting a PXI controller and TargetList vi stops The Call By Reference Node connector output PXI Target is then used to update the corresponding element of the large cluster that is passed from one iteration of the outer While Loop to the next via the top shift register Closing the VI reference does not close the front panel window of TargetList vi Thus the VI and changes to its controls made by the user remain in memory After a new type specifier VI Refnum to Embedded llb TargetList vi is obtained the method Make Current Values Default is invoked and these changes to default values are made permanent by saving the VI with the method Save Instrument Finally the front panel window of TargetList vi is closed and by closing the VI reference the VI is removed from memory save Instrument Selecting a new PXI controller for G clamp requires re initialization of G clamp vi Thus the queue is provided with the string Initialize As Initialize will create a new application reference to the LabVIEW RT Engine on the newly selected PXI controller the old target
67. formed thus data can be lost Since only one VI can access a global variable at a time it can cause priority inversions which in turn cause jitter or increase execution time in the time critical loop Functional globals have a similar behavior However with the RT FIFO a write and a read can be performed at the same time Also the RT FIFO acts like a fixed size queue so that data elements that you write to an RT FIFO do not overwrite previous elements unless the RT FIFO is full in which case the oldest element is over written The RT FIFO can be a lossy communication if the reader does not read elements from the FIFO before the FIFO fills up The advantage of using the RT FIFO is that even if the reader pauses momentarily and multiple writes to the RT FIFO occur during that time data is not lost as long as the reader can catch up and read the elements out of the RT FIFO before it fills up This document will focus on the third method of communication between VIs the RT FIFO Using RT FIFO The RT FIFO is simple to use Its use involves creating the RT FIFO in one VI and either passing the RT FIFO reference to the other VI or opening a reference to the RT FIFO in the another VI Then writes to the RT FIFO are performed in one VI and reads from the RT FIFO performed in another VI and finally the RT FIFO is deleted Figure 2 shows an example of using the RT FIFO although in this example data is transferred to and from the same VI type FIFO
68. forms analog to digital conversions Even if for some reason the feedback loop transiently lags behind it is able to ignore outdated data and to catch up by flushing the FIFO buffer and using only the newest data Note that the data in input of AI SingleScan vi is set to a 1 D array with 2 elements 1 e an array with the same number of elements as will be put out by AI SingleScan vi This improves performance of AI SingleScan vi by pre allocating a block of memory for the data and thus avoiding invocation of the memory manager The actual values in the 1 D array meaningless and are ignored by AI SingleScan vi The raw voltage data obtained from AI SingleScan vi are converted to mV and pA The two values are stored separately in two 1 D arrays of SGL that had been initialized by and passed to V clamp DQA vi by its caller IV Relation Sub vi DC command Vm Buffer and Template Im Buffer Before the new values are stored in these arrays with Replace Array Subset from both arrays the element at index current loop iteration count 2 For the 16 Bit E Series Multifunction DAQ boards the length of this buffer is 512 samples 2 We haven t found anywhere an explanation for why it would make sense to read as often as possible the oldest data and to read the newest data and flush the FIFO only when necessary We presume that reading from the head of the queue is still faster than flushing a queue and obtaining the newest element even if th
69. geted to the host computer it is not possible to apply LabVIEW debugging tools like probes execution highlighting etc to experiment module VIs and their sub VIs as these are executing on the embedded computer gt Sections 3 and 5 Attempts to circumvent the problem of finite memory by performing file IO loading the template and saving acquired traces on the fly 1 e while the experiment is in progress were unsuccessful when running the dynamic clamp on a PXI 8170 controller at a feedback loop rate of 20 kHz This might become an option in the future when faster processors and or hard drives become available Page 7 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 4 The user interface G clamp VI G clamp vi 1s a queue driven state machine A While Loop loops continually as long as G clamp is running and executes exactly one case of a Case Structure during each iteration The selector determining which case to execute is a string derived from a queue which operates as a FIFO buffer first in first out If the queue is empty Remove Queue Element vi times out after 1 ms and the default case Check Controls is executed The main purpose of the default case Check Controls is to detect user interactions with front panel controls using an Event Structure and to add the appropriate string to the queue The Event Structure processes all defined user events that accumulated before G clamp vi execution got to the
70. h Pattern as shown in Error Reference source not found is unwired In this instance ScriptAnalyzer VI only uses the numerical value to set the count N terminal of the large For Loop to the intended number of iterations The remainder of the script string is then analyzed by repeating this basic mechanism again and again In most cases 1 e whenever the script continues in a new line the first Page 60 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide character in the remaining script string is a Line Feed LF or Carriage Return CR To get rid of this character the String Subset function is employed Figure 8 2 Figure 8 2 script 1st line for x After having determined the number of iterations ScriptAnalyzer VI proceeds with determining the total length of the intended command sequence This is done in a While Loop by summing up all numbers following a wait command After the number of iterations and the total command length has been determined a 2 dimensional array for the command signal is initialized with zeroes Obtaining the first wait value of the script initializes a pointer indexing the position from which to start replacing the zeroes with a new voltage value After the first two lines of the script have been interpreted the remainder of the script enters the large For Loop of iterations and the enclosed While loop The While loop operates on the presumption that the remaining script consists
71. h vi has been deleted from Embedded lib Page 84 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide Embedded llb Synaptic Gain vi A For Loop which concatenates the names of the used template files into one string together with result string indicator TemplateFile has been deleted as that information 1s used nowhere Embedded llibiLoadTemplates vi An unused EOF has been removed Embedded llbiSynaptic Gain Sub vi The 1 D array of cluster for the time stamps has been set to a length of exactly equal to the template with a maximum of 1000000 G clamp IIbiG clamp vi A menu item Help has been added to the custom run time menu The sub item About G clamp is a user item and is dealt with in a new case About G clamp The main purpose of the dialog presented is to give the G clamp version number The sub item About LabVIEW is an application item automatically handled by LabVIEW and therefore does not require any additional programming It gives the LabVIEW version number and other information 02 23 2004 G clamp v1 2 The use of template files of type GTM with the Synaptic Gain module has been phased out This allowed the following code simplifications o In Embedded llb List Templates vi The gtm element of the 1 D array of strings feeding into the pattern input of List Directory has been deleted Synaptic Gain vi Determining the file type to determine the he
72. he array by one element with information about a new PXI controller finish execution and writing information about the selected PXI controller to the indicator PXI Target Page 62 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide E i Done Value Changed e A a The caller of TargetList vi G clamp vi will invoke the method Make Current Values Default and subsequently Save VI This will make any additions to or deletions from the list of PXI controllers contained in the 1 D array of cluster permanent as well as any changes in a cluster element This also allows G clamp vi during initialization to obtain the information about the last PXI controller by invoking the method Get Control Value on the PXI Target indicator of TargetList vi see 4 1 1 Initialize Note that the time out input of the Event Structure is unwired 1 e the Event Structure never times out It will wait until a user event occurs thus keeping G clamp idle and the computer CPU free to do other things Page 63 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 9 Adding a new experiment module For purpose of illustration the new experiment module will be named NewModule vi throughout this section The discription will first focus on a new experiment module that does not require new parameters and therefore new front panel controls on the user interface sections 9 1 and 9 2 Implementation of
73. he elements of a 1 D array of variants to the experiment module VI Thus an easy way to add new experiment specific parameters is to bundle them all into a cluster convert the cluster to a variant and add the variant to the 1 D array of variants that is build in the experiment module specific case and that is successively transferred to the experiment module VI This method requires that in the experiment module VI the variant 1s converted back to a cluster and the individual parameters accessed by unbundling Note that the name of the variant control in the experiment module VI has to be added in G clamp vi to the 1 D array of strings that feeds into the Control Name input of the Set Control Value Invoke Node karting En on remote machine eh Set Control value oon i el Control Mame E m YE F Hs _ NewParameters p oo s M a E e a ele Flattened Data Page 70 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 10 Non LabVIEW files G clamp uses a number of files VIs DLLs that are not part of the LabVIEW distribution and that have been downloaded from NIs website 10 1 RT FIFOs RT FIFOs allow transfer of data in and out of the time critical feedback loop They are implemented as a set of VIs in RTFIFO LLB which draw on a dynamic link library NBFIFO DLL To download these files together with some example VIs click on the link at the end of the tutorial
74. he template file contains only single precision numbers SGLs 1 e 4 bytes number The first Read File returns the header of the template by reading 19 SGLs from the beginning of the file With the pos mode and the pos offset inputs unwired the second Read File starts reading the template proper from where the first Read File left the file mark when 1t finished Note that the only information actually used from the header 1s 1ts first element 1 e the sample interval Page 45 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide NI Eee Bs 2 E E dl gt a O 7 OFEH FILE FILE ES FILE ELKE a OO Gel az 0 0 po esa E 1000 00 S 00 DEL pa al A Dykes S 7 1 2 Gsyn Threshold Sub vi Gsyn Threshold Sub vi receives the template via the RT FIFO Result Data Queue before the While Loop starts executing Scaling of the template is done within the While Loop by multiplying the template with the mean of two shift registers initialized with the user specified values of the controls Gmin and Gmax Result Daka Queue 4 c E Contre Values After a data acquisition iteration has been performed the voltage trace is analyzed to determine whether the virtual synapse elicited an action potential Array Max amp Min 1s applied to the 1 D array and the maximum value is checked against 0 Thus the analysis is a simple threshold comparison with the threshold value S
75. his array would be created at the beginning of the program and passed into the loop where Al SingleScan is located See Also Preallocating Arrays for Deterministic Loops Using the Al Single Scan Opcode Al SingleScan has an input called opcode which specifies the type of data retrieval the VI performs There are 5 opcodes 0 Do not change the opcode setting default input 1 Read oldest data default setting 2 Read newest data 3 Set the value of the data remaining indicator only no data is read 4 Empty the FIFO only for timed nonbuffered acquisition only No data is returned The two of most interest for LabVIEW Real Time applications are 1 Read oldest data and 2 Read newest data When performing nonbuffered input read oldest data will cause Al SingleScan to return the oldest scan from the FIFO after the next scan clock active edge arrive and leave the other scans in the FIFO Read newest data will return the scan that gets acquired at the next scan clock active edge and clear the FIFO of old data For single point real time applications Read newest data should be used at least on the first iteration so that the FIFO is cleared of any scans that have arrived between the time that Al Start was called and the first call of Al SingleScan After the first iteration Read oldest data can be used in conjunction with data remaining to monitor if the VI is keeping real time as will be discussed next Determining Real Time
76. ime interval between data points dt extracted from the header Using auto indexing for the output of the For Loop the voltage and current waveforms are assembled into a 1 D array of waveforms which feeds directly into the waveform graph indicator Waveform Graph on the front panel to display the two traces All other header information extracted twice in the For Loop exits the For Loop without auto indexing Note that the content of the header and its size differ between experiment modules Therefore the arrangement of operations performed in the For Loop varies somewhat between the experiment module specific cases of the Case Structure in Process The case for the Synaptic Gain module differs even more as in this module transfer of the recorded traces to the host computer is optional see Synaptic Gain under Experiment module specifics below All headers contain although at different positions within the header the true sample interval going through a Reciprocal and fed into the front panel indicator A D rate and the RT loop performance information fed into the front panel indicator RT Loop Info 2 The 1 D array of waveforms containing the voltage and current trace is added as new element to a 2 D array of waveforms that is buffered in the hidden waveform indicator Output Array After the experiment module VI has finished executing this buffer serves as the source for displaying
77. imeDate vi see section 10 3 4 1 3 Check Controls This 1s the default case that executes whenever the queue 1s empty The central element in this case 1s an Event Structure which handles 4 different kinds of user interactions with front panel elements in 5 of 1ts 6 cases l Clear Graph clears the graph in the Synaptic Gain page by providing its Value property with an empty array The empty array also resets fpre and Gain two controls used as temporary data buffers and accessed here via Local Variables 2 Menu Selection User handles selections made from the G clamp run time menu A Match Pattern first determines whether a selection has been made from the menu item Function If this is the case the front panel window title of G clamp vi is updated to reflect the chosen experiment module the variable Exp Type is updated accordingly and the queue is provided with the string Enable Disable Controls 7 An easy way to specify the correct type is to right click while pointing on the VI Refnum control select Select VI Server Class gt Browse and to choose the VI that 1s to be called by the Call By Reference Node Keep in mind that any change in the connector pane of the called VI requires a new type specification of the VI refnum control Page 13 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide E Hal 2 Menu Selection User ItemPath o E JEnable Disable
78. index input index 0 of a Delete From Array Delete From Array takes the 2 D array that is the Value property of Selected templates containing elements only along one dimension 1 e the first column and because its disabled column index input index 1 1t deletes one 1 at length input complete row Available templates Selected templates Bl A Selected templates Page 19 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 4 1 8 Start ExpModule Step1 This case 1s preparatory and precedes the actual start of a data acquisition Start ExpModule Step2 It transfers the values of several controls to corresponding elements of the large cluster that is passed from one iteration of the outer While Loop to the next via the top shift register To free memory on the host computer it clears several data buffers and the trace display by feeding them empty inputs Incase of the Gsyn Threshold and the Synaptic Gain module 1t checks whether a template has been selected On this condition rests whether execution will proceed with the Start ExpModule Step2 case 4 1 9 Start ExpModule Step2 This case uses the application reference to the LabVIEW RT Engine on the PXI controller which had been obtained in the Initialize case to open a VI reference to the experiment module VI It then invokes the method Set Control Value to provide the experiment module VI with all the user spe
79. ing and serves only as a means to exit the Event Structure without waiting indefinitely for a user event P z Hal 0 Timeout The time out value for the Event Structure is dependent on the state of G clamp If the queue already contains elements checked by Get Queue Status vi or if the Boolean variable DAQ in process indicates an ongoing experiment the Event Structure waits only ms for a user event thus allowing the pending actions to proceed quickly If a data acquisition is in process the queue receives the string New Data after the Event Structure has completed Otherwise the Event Structure waits for 250 ms 4 1 4 Enable Disable Controls This case executes after a change of the experiment module to make those controls necessary for the module visible and enabled while disabling or making invisible This works because the cursors in the IV Relation graph are set up as Snap to point i e wherever they get dragged by the user their x and y coordinates always snap to the closest data point Page 15 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide unneeded controls Thus this case mainly sets the property Disabled and the property Visible of many controls to new values For many controls these settings are stored in an array of clusters with one array element cluster containing the settings specific to one experiment module The correct cluster is obtained by
80. intain its content from one iteration of the inner For Loop to the next After a trace has been received completely the 1 D array of SGLs is converted to a waveform and a 1 D array of waveforms is obtained using auto indexing of the output of the outer For Loop V clamp Structure of the 1 D array of DBLs Waveform Graph o index O start time of the trace acquisition coded as seconds elapses since 12 00 AM o index 1 reciprocal of the actual sample rate Hz of the analog input operation o index 2 not used set to zero o index 3 n 4 voltage and current trace respectively o index n 3 n RT loop performance information Page 30 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide Each experiment module has its own data file format These are documented in the G clamp User Manual 4 1 14 Stop Closes the TCP connection and the reference to the experiment module VI Adds a Plot all to the queue if more than iteration has been performed Adds a Start ExpModule Step to the queue if two conditions are fulfilled o Selected templates is not empty and o the current experiment module is Gsyn Threshold or Synaptic Gain Sets the variable DAQ in process to FALSE and thus stops the default case Check Controls from adding a New Data to the queue 4 1 15 Plot all Replaces the last set of acquired traces visible in the front panel waveform graph
81. l template Page 49 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 7 2 2 Synaptic Gain Sub vi Synaptic Gain Sub vi converts the 2 D array with the template into a 1 D array before 1t 1s handed to G clamp DQA vi This makes it easier to retrieve individual array elements in the feedback control loop as the only index required can be obtained without any computation from the iteration 1 terminal of the While Loop in G clamp DQA Vi Changing the dimensionality of an array does not require a new memory allocation as the number of elements stays the same and therefore the same memory space is reused Synaptic Gain Sub vi also pre allocates memory for the voltage trace to be acquired by initializing a 1 D array of SGLs and for the time stamps collected in the feedback control loop Note that this 1 D array of cluster of unsigned long integers U 32 is as long as the template but does not exceed 1 000 000 elements As it is unlikely that loop rates change during a data acquisition collecting more than 1 million time stamps will provide no further information about deterministic execution of the control loop and the restriction to 1 million prevents excessive memory consumption by the time stamps Thus although the feedback loop will still collect a time stamp during each iteration each value in excess of 1 million will be discarded Once G clamp DQA vi has finished the acquired voltage trace 1s analyzed to determine the num
82. lable After all shift registers have been updated the While loop starts all over with AI SingleScan vi waiting for the next trigger from the scan clock What happens during the time until that trigger arrives depends on the setting for UseSleepingTimedNonBuffered in the file ni rt ini on the PXI controller see also section 11 1 If UseSleepingTimedNonBuffered FALSE as is recommended in the G clamp installation instructions given in the G clamp User Manual to achieve maximum loop rates the feedback loop will block all other processes running in parallel e g the communication loop from proceeding As the communication loop has to wait for the end of a data acquisition iteration anyway before it can communicate something to the host computer this is not a loss If UseSleepingTimedNonBuffered TRUE AI SingleScan vi acts like a wait command until the next analog to digital conversion is triggered by the scan clock Until then the thread in which the feedback loop runs 1s effectively put to 2 Alternatively AI control config vi can be broken apart into its constituent sub VIs so that everything except AI Start vi is performed once outside the While loop in Sub vi and AI Start vi remains as the last operation before the While Loop in G clamp DQA vi see also section 7 3 1 V clamp Sub vi for an example Page 42 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide sleep and the PXI controller s CPU is free to run
83. le Loop gt AI Start vi is called with its number of scans to acquire input set to 0 indicating continuous data acquisition until the task 1s cleared with AI Clear vi The actual scan rate output of AI Start vi is converted to sample interval length to provide the dt ms input of V dependent Conductances vi Page 39 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide Once AI Start vi has been called the data acquisition board reads the specified analog input channels and performs analog to digital conversions at the specified rate The result of each analog to digital conversion is written to an onboard FIFO buffer from which AI SingleScan vi triggered by the scan clock on the data acquisition board that times the analog to digital conversions retrieves one element at a time At the first iteration of the While Loop AI SingleScan vi reads the newest data from the FIFO buffer effectively flushing the buffer of all data that accumulated in 1t between execution of Al Start vi and the first call of AI SingleScan vi The data remaining output of AI SingleScan vi indicates now an empty FIFO and gives a 0 which via a shift register is used during the next iteration of the While Loop to set the opcode input of to AI SingleScan vi to read the oldest data in the FIFO Thus data remaining monitors whether the While Loop keeps up with the speed at which the data acquisition board per
84. lements of the 15 element 1 D array of SGLs DAQ Control Values of the cluster Cluster with control values other than derived from the cluster control Settings 35 Point at the index control at the top left to select the whole control If you point inside the cluster on one of its elements controls the selected menu function Make Current Value Default will operate only on the control you were pointing at Page 68 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 6 In the Case Structure of the Start ExpModule Step2 case a case for the new experiment module has to be added The easiest way to do this is to make a duplicate of an existing case that rn eo T EA A er r most closely reflects what the amp NewModule vih new case should look like To do W ra J so move to the case you want to Selected templates duplicate and right click while pointing on the frame of the Case Structure In the upcoming menu select Duplicate Case At minimum one change has to be done in the new case In the string constant exiting the Case Structure at the top right corner replace the name of the experiment module VI with the name of the new VI NewModule vi If the new experiment module has new parameters that require new front panel controls the content of the new case might require further modifications For that see the next section 9 3 New control parameters 7 In the Case Structure of th
85. m Graph Property Node a write property Xscale ScaleFit set to 0 1 e do not autoscale has been added Now the final plotting of all acquired traces performs much Page 86 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide waveform Graph EI j Ack Scl Scale ScaleFit oj Scale ScaleFit G clamp lIb G clamp vi In the case of the 0 000 H scale Range Pesa 0 001 HP Scale Minimum T Process case processing data from the Synaptic a 7 A T Gain module the 1 D arrays of string indicators 72 TraceFileName and UsedTemplate have been deleted Using 1 D arrays was a leftover from a time when GAJ files stored information from a series of Synaptic Gain experiments Also in frame 2 of the Sequence Structure the For Loop performing the repeated File Write operations for the now obsolete saving of information from a series of Synaptic Gain experiments has been deleted Thus all the parameters saved are now simple values and not any longer elements derived from 1 D arrays Therefore these changes also take care of a bug which resulted in saving of the oldest fpre and Gain values instead of the newest if the 1 D arrays fpre and Gain were not emptied with the Clear Graph control after each Synaptic Gain experiment faster as long graph updates when the x axis 1s set to auto scale are now shortened by displaying only tiny stretches G clamp llb G
86. mplate o index 3 n 4 voltage and current trace respectively o index n 3 n RT loop performance information Synaptic Gain The two 1 D arrays of DBLs fpre and Gain provide the xy graph Gain with input and serve as buffers before the data get saved to file fpre and Gain are re initialized with an empty array in the Clear Graph case of the Event Structure in the Check Controls case 1 e by the user with the control Clear Graph Because of the long templates possible with this experiment module a transmission of voltage and current trace to the host computer is optional and done via a separate TCP transmission in the Process case and b saving of the traces to file occurs on the PXI controller while analysis results are saved in a separate file on the host computer Page 28 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide The two transmissions in the New Data case are used for header information only and each of the two transmissions has different content The 2 D array of DBLs Waveform Graph thus has the structure o index 0 0 mean presynaptic activity rate fpre Hz o index 0 1 gain o index 0 2 ending time of the trace acquisition coded as seconds elapses since 12 00 AM o index 0 3 reciprocal of the actual sample rate Hz of the analog input operation o index 1 0 3 RT loop performance information To have identical
87. n the loop is executed and upon the next iteration the Al SingleScan VI node goes to sleep again to repeat the cycle This document will discuss some of the features of Al Single Scan in relation to LabVIEW Real Time Table of Contents Using Sleep Mode to Time Loops Preallocating arrays for Control Loops Using the Al Single Scan Opcode Determining Real Time Status Using the Data Remaining Parameter Verifying the Sleep Mode Configuration Using Sleep Mode to Time Loops In LabVIEW for Windows when doing nonbuffered analog input buffer size 0 Al SingleScan will return immediately if there is data in the FIFO of the DAQ board If there is no data in the FIFO then Al SingleScan will wait until data arrives in the FIFO before returning In LabVIEW Real Time starting with NI DAQ 6 7 0 Al SingleScan has a sleep mode which is enabled by default in the NI RT INI file When sleep mode is enabled and you are performing nonbuffered analog input when Al SingleScan is called it will sleep until the next active scan clock edge occurs Only then will Al SingleScan return even if the FIFO had data when Al SingleScan was called While Al SingleScan is waiting for the next active scan clock edge it causes the entire thread it is in to sleep A thread is comprised of all the VIs and other processes in the same execution system at the same priority so the VI Al SingleScan is in and all other Vis set to the same priority and execution system as th
88. ng handout Large data objects in LabVIEW both downloadable from NIs website as pdfs tunnels used to route data sets through loops create a data copy each time the loop iterates For Loops are used to break the File I O and TCP IP operations into smaller tasks done repeatedly While we think that the same memory space is used over and over again as long as the size of the data set stays constant it is possible that each creation of a copy or memory allocation in other words invokes the memory manager and thus slows down the whole process This would explain the comparatively slow saving of data we observe in Synaptic Gain vi which is much slower than what we expected after making sure that writing is done in multiples of 512 bytes and which is much slower than the reading of the template file s at the beginning of the experiment Damien Gray s advice is to use shift registers which will make a memory copy only the first time the loop executes Page 54 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide A Match Pattern searches for the first occurrence of a string expression matching a number in the script which is supposed to come in the first line after a For command The unflattened script 1s also passed on to V clamp Sub vi for interpretation by ScriptAnalyzer vi 7 3 1 V clamp Sub vi V clamp Sub vi does not use the feedback loop module G clamp DQA vi Instead a simplified feedback loop is integrated direc
89. ng state of development This year for example we added a new Page 4 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide V clamp experiment module so that one can conduct hybrid experiments that switch between voltage clamp and dynamic current clamp modes We have also supported other users in modifying the existing experiment modules for their specific needs Several ideas under consideration for inclusion in a future release of G clamp version 2 include The ability to generate irregularly timed stimulus pulses that can drive nerve stimulation and thereby mimic the activity represented by synaptic template files The implementation of synaptic template files that can create multiple types of virtual synapses e g excitatory and inhibitory NMDA vs AMPA type kinetics and voltage sensitivity Generation of an experimental logging function This feature would automatically generate a text file that contains a running record of all events in an experiment including the parameters used It would also include a new comments field that could be used to track additional information about the experiment e g drug applications The format of the log file could be either a simple text file or a formatted file with fields whose content could be be bulk loaded into a relational database Simplify the procedure for adding new experiment modules This would require changing the way in which experiment modules are integrate
90. ni rt g clamp on the PXI controller Create Plugin List vi has now much fewer VIs to test and is done much faster resulting in faster initialization when G clamp vi is started Accordingly the directory input of Create Plugin List vi is now provided with the string constant gModules instead of Embedded lb in List Templates vi In order to make this change work the path information to the conductance module VIs had to be changed in Embedded llb V dependent Conductances vi which is the caller of the conductance module VIs This was done by opening Embedded llb V dependent Conductances vi and all implemented conductance module Vis gNa vi gKdr vi gKM vi gLeak vi and gKA vi on the host computer and using the Save as option to save the conductance module VIs into a directory c ni rt g clamp gModules on the host computer Upon subsequent closing of Embedded llb V dependent Conductances vi the saving requested by LabVIEW of V dependent Conductances vi because of the change in the location of the sub VIs is accepted and the conductance module VIs can be deleted from Embedded Ilb The updated Embedded llb replaces the library on the PXI controller Embedded llb Gsyn Threshold vi Embedded llbiGsyn Threshold Sub vi and Embedded llb Synaptic Gain vi The sub VI GetTemplateFilepath vi has been replaced by a Build Path with the path constant c ni rt g clamp template as base path input and GetTemplateFilepat
91. nnnnnnnnnnnnnnss 6 Thecuser interface G clamp Vi stat ii ita 8 4 1 G clamp start and program initialization ooooooonnnnnccnnnnnnnnnnnnnnnnonononnannnncnnnnnnnos 8 4 1 1 PP UE II A 9 4 1 2 Miale a A A eT Ca 11 4 1 3 CREER 0 10 0 lt P PRO Pron pagascen a tec eecsencnseetabataaa 13 4 1 4 Enable Disable COntOlS erat ala se 15 4 1 5 EXT as 17 4 1 6 DAQ Board ConfIguratlON cccccccccccnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn 18 417 Selecion Modifie diens a E stab ynieneeeuaeeellaeenets 18 4 1 8 Start ExpModule de R 20 4 1 9 Start EXpModule Siep i 20 FO AEA ALC en e O cel adalad Sersiaeiten anise uoractiaesadetatces 22 ANN O A A E E an E eteuueue 22 A A SOU a E A A OA AAE 24 Alla Process A A a a 25 A NID aia 31 WAS A A A NT Serene Tee eee 31 ALO ta ee 32 Alr DON eeaeee A aah ascbetianen E A 32 An exemplar experiment module IV Relation Vl ooooonnnnnnnnnnnnnnnnooncncnnnnnnnnnnn o 33 5 1 Operation of the communication loop ooccccccnnnnnnnnooccnononnnnnononanococnnnnnnnnnnnoo 35 32 IV REKOSO VL ae a N E A 35 5321 The RT feedback module G clamp DOA Vl occncnnnnnocnccnnnnonnnnnnnonoccconnnnnnos 39 PEIOTINIES and execution SS CMS dat 44 Other experiment modules Es 45 7 1 E Mi ll of SRON A E o ET O O A vn eee ee one 45 7 1 1 e A ee eee A eee ne Ree an Seer ere ee 45 PAZ Gisy Pre sh Old SUD Vlad 46 12 Synapte Gall dad did 47 Tal kogdT emplie SN herr EA mes eossuuseuerieaanees 48 R22 Synaphe Gdin SUD
92. o articles from National Instruments knowledge base explains the function of the parameter NI DAQ UseSleepingTimedNonBuffered FALSE in the file c ni rt 1ni on the PXI controller How Can I Achieve Control Loop Rates Faster Than 1 kHz Using LabVIEW Real Time Product Group DAQ Documentation Product Name NI DAQ Problem am using LabVIEW Real Time s Wait Until Next ms Multiple function to control my loop cycle time however because the function has a 1 ms resolution the fastest rate can achieve is 1 kHz or 1 ms loop cycle time Are there any Vis in LabVIEW Real Time that will allow me to achieve a faster loop rate Solution Using the Wait and Wait Until Next ms Multiple functions a LabVIEW Real Time programmer can achieve loop rates of 1000 Hz Alternately loop rates can achieve their maximum rate if there is no delay in the loop however without a delay we cannot control the rate of the loop accurately Starting with NI DAQ 6 7 0 Al SingleScan can anchor software timing to the onboard scanclock signal on E Series DAQ boards in the real time operating system This new feature lets control applications harness hardware determinism in LabVIEW Real Time When a DAQ board is configured for a certain scan rate and is ready to begin sampling the onboard scanclock controls the timing of analog to digital A D conversions Each scanclock cycle corresponds to a single scan across all channels in the scan list Al SingleScan simply colle
93. o consecutive transmissions via the TCP connection between the experiment module VI and G clamp vi The first row of data in Waveform Graph represents the voltage trace recorded by the experiment module preceded by a header containing additional information about the experiment The second row of data contains the recorded current trace preceded by an identical copy of the header used with the voltage trace 1 Thus the first task in B processing the received data is to separate the ha LLL k trace from the header and to extract the information contained in the header This is done in a For Loop which uses auto indexing of the 2 D array of DBLs to set the number of iterations and to separate the two sets of data Index Array is then used to obtain individual values from the header The data set 1s then reduced with an Page 25 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide Array Subset that chops off the leading portion of the data set The output of Array Subset consists of the rest of the header plus the trace The remaining header consists of information that 1s used in the form of a 1 D array Thus a Split 1D Array can be used to separate this part of the header from the trace The 1 D array of DBLs representing the trace is then converted to the LabVIEW data type waveform by feeding it into a Build Waveform together with two DBLs representing the time when the trace was recorded t0 and the t
94. om c ni rt g clamp Embedded llb and save it immediately under a new name NewModule vi back into Embedded llb with File gt Save As Page 64 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide Modify NewModule vi so that it performs your experiment Use File gt Save with Options to save the final version of the experiment module in Embedded llb Use the Custom Save option and save the entire hierarchy including vi lib files and external subroutines With this custom save all LabVIEW system libraries and external subroutines not present on the PXI E Save with Options F qn Changed vIs E Development Distribution e Application gett Distribution Fey Custom 2 Save Zz Save For 60 Previous no Template Save Options For G clamp vi Selected Options f o new location single prompt W Save entire hierarchy M Include vi lib Files Include external subroutines M Include run time menus No password change Remove passwords F Apply new password Remove diagrams Copy Embedded llb back into c n1 rt g clamp on the PXI controller 9 2 Adding the module to G clamp vi 1 From the G clamp vi menu use Edit gt Run Time Menu to start the menu editor Under the menu item Function add the name of the new experiment module without the extension vi at the end of the list of implemented experiment modules 4 Tf you receive an error message
95. on page and thus by dragging the cursors With this change the calculation is only done when the user requests it and not any more each time the default case Check Controls executes Page 82 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide old new aHaj 5 IY Relation Mouse Up Ctl Ref PlatMods G clamp llb G clamp vi All code relating to the property Row Headers of the Table indicator Selected templates has been deleted as it didn t serve any purpose in G clamp vi G clamp llb G clamp vi In the Start Failed case forcing dataflow by using the error out output of TCP Close Connection at the error in input of Close LV Object Reference has been replaced by placing Close LV Object Reference into a Sequence Structure which executes only after receiving the error out output of TCP Close Connection The reason is that in the old scheme a failure to establish the TCP connection in the Start ExpModule Step2 case would result in an error reported by TCP Close Connection Passing an error on to Close LV Object Reference would prevent Close LV Object Reference to function properly 1 e the reference to the experiment module VI would remain open General Error Handler vi has been moved from the Start Failed case to the Start ExpModule Step2 case and replaces the Unbundle function in that case that 1s used to obtain the error status G clamp lIlb G clamp vi
96. ontains Processor speed MHz as sub element and AO Cluster of the large cluster also contains device as sub element The correct values for these sub elements have been obtained already see section 2 in 4 1 1 Initialize and are now overwritten with wrong settings derived from AnalogInOutConfig vi To maintain the correct settings these are read out of the large cluster and used to replace the incorrect settings after Al Cluster and AO Cluster are updated with the values from AnalogInOutConfig vi Al Cluster Processor speed MHz Na AI Cluster Processor speed MHz a 40 Cluster device AD Cluster device JE IAE A are ao Cluster Y 2 The final step in G clamp initialization is the synchronization of date and time between host computer and PXI controller This is done by using a Call By Reference Node to execute Embedded llb SetTimeDate vi on the PXI controller while at the same time providing it with the current host computer date and time as Start parameters Page 12 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide Fei iaie cil day of month To use a Call By Reference Node Open VI Reference has to be provided with a VI Refnum control The VI Refnum control acts as a type specifier so that the Call By Reference Node can take on a pattern of input and output connectors identical to the connector pane of the VI to be called For more information about SetT
97. ot use a cache This means that every write and read operation requires an access to the disk How can optimize file I O in LabVIEW RT Since LabVIEW RT does not use a cache we need to minimize the access time to our disk The most important thing to consider is to write out data one sector at a time In LabVIEW RT on a PXI controller the sector size is 512 bytes The reason for this is that every read and write operation will always execute in 512 byte increments If our application requests a write of 30 bytes the OS would have to first read the entire 512 byte sector replace the 30 bytes you are writing and then write the entire sector back Similarly if you wanted to read 30 bytes the OS would have to read an entire 512 byte sector first then pull out the 30 bytes needed In fact it takes less time to read or write 512 bytes than it does to read or write smaller byte sizes The best performance will be observed if you write 512 bytes at a time and remain aligned with the file sectors To ensure that you are starting your write or read at the beginning of a sector keep your offset restricted to multiples of 512 0 512 1024 etc If you wire an input that is not a multiple of 512 then you are no longer aligned with the file sectors For example if you wire an input offset of 1 then you actually will have to write to two separate disk sectors On one sector you ll write 511 bytes and on the other you ll write the left over 1 byte B
98. other threads e g the communication loop Once the While Loop has finished the analog input and output operations are cleared with AI Clear vi and AO Clear vi Most importantly this stops the data acquisition board from doing further analog to digital conversions and causing a FIFO overflow which would rest the whole DAQ board Thus the tasks Ds handed down from Sub vi can be re used for the next data acquisition iteration without going through the whole configuration process again Finally the time stamps are analyzed to obtain the RT Loop Info Before the 1 D array of time stamps is handed to Timing Analysis vi the first 200 elements are chopped off with a Delete From Array This serves to eliminate intervals longer than the acquisition rate bound to happen at the beginning of the data acquisition It can take several cycles of the feedback loop before all the hardware processes associated with analog input and output are correctly initialized and working at a regular rate 2 For this reason LabVIEW RT example VIs usually set the opcode input of AI SingleScan vi to read newest data for the first 10 cycles of the control loop As these examples usually run at much lower speeds and G clamp is supposed to go to maximum speeds we thought it saver to discard more but potentially extremely short cycles to give the system the time it needs before it runs regularly Page 43 of 88 Kullmann and Horn 2004b G clamp Programmer
99. ou are changing the time of an RT Engine target LabVIEW Real Time to your RT Engine and run settimedate vi This VI will change the time in the computer s BIOS at the same time it changes the operating system s time When building an application using this VI the DLLs must be included as support files When using this VI on the FP 2000 2010 you will want to disable the time synchronization service on the FP 20xx This service sets the system time on the FP 20xx to the GMT timezone and it doesn t account for differences with respect to your time zone You can disable the synchronization service by setting the Time Synch Server IP address to 0 0 0 0 This VI does not work correctly on laptop computers It sets the time to hour 7 Software Requirements Application Software LabVIEW 6 0 Language s LabVIEW Download Example Download settimedate zip 155 kilobyte s Comments I don t understand what evi _lvrt dll is needed for We found that for SetTimeDate vi to work Settime dll is sufficient Date and time are system properties on Windows computers To use SetTimeDate vi on a Windows computer thus requires to be logged in with administrator privileges The While Loop in SetTimeDate vi tends to monopolize the CPU and should be slowed down by including a wait function Page 75 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 11 LabVIEW RT specifics 11 1 ATI SingleScan s sleep mode The following tw
100. rations performed by this VI are detailed in section 5 2 1 5 After the real time feedback loop module G clamp DQA vi has finished executing the two acquired traces voltage and current are assembled into a 2 D array In a For Loop each trace together with other header information is used to build a new 1 D array For the exact content of the header see section 4 1 13 sub section 2 Experiment module specifics This new array 1s then added to the Result Data Queue from which the communication loop reads it and transmits it to G clamp vi on the host 19 computer While in G clamp DQA vi great care has been taken to use only pre allocated memory buffers of exactly the required size to avoid invocation of the LabVIEW memory manager and thus avoid violation of determinism the treatment of the acquired traces here violates this principle Each use of the Build Array function results in a memory duplication and the same is possibly true for the entry nodes of the For Loop A better way would be to pre allocate buffers of length of data points of header elements G clamp DQA vi would place a trace in array elements 0 to trace length 1 After G clamp DQA vi a number of Replace Array Subset functions would replace the final array elements with the header information thus in effect changing the header to a tail and requiring a corresponding change in the Process case of G clamp vi To get rid of the For Loop this would nee
101. ray Subset function You must implement your custom application in a similar manner to properly measure its software determinism NOTE In order for this timing method to function properly you must provide your processor speed This method results in erroneous data when running on laptops because laptops frequently adjust the processor clock speed dynamically to conserve energy when there is no load To remedy this problem place an empty running While loop set at NORMAL PRIORITY in parallel with the application being timed The RDTSC instruction also returns erroneous data from dual processor machines because the instruction does not always grab the time stamp from the same processor Each processor s Time Stamp Counter is running independent of the other Software Requirements Application Software LabVIEW 5 1 Toolkits and Add ons Additional Software Language s LabVIEW Download Example Download rdtsc zip 67 kilobyte s Page 74 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 10 3 SetTimeDate From National Instruments website Setting the System Date and Time This VI sets the system time and date on your PC or PXI computer running either Windows or the LabVIEW Real Time Operating System It calls a DLL called Settime dll The DLL was built in LabWindows CVI Place the cvi_lvrt dll from the attached zip file in your LabVIEW directory National Instruments LabVIEW and then run settimedate vi If y
102. recting it to the case that checks for the availability of new data New Data Transferring experiment parameters to the experiment module VI Related parameters mostly derived from the large cluster that is passed from one iteration of the outer While Loop to the next via the top shift register are bundled together in an array or a cluster that is then converted to the LabVIEW data type variant In the Case Structure all variants relevant to the selected experiment module are then assembled into a 1 D array which is used to auto index together with a 1 D array of strings representing the control names the For Loop in which the method Set Control Value is invoked on the experiment module VI E ni rtig clampiEmbedded Il While this scheme requires converting the parameters back into their original data types in the experiment module VI 1t offers a flexible way to deal with different types and numbers of parameters required for different experiment modules Changes to the number of elements in a cluster or array of related parameters are taken care of automatically by the data type conversion to variant Re sizing the Build Array function and exploiting the auto indexing of the For Loop adjusts to changes in the number of variants Page 21 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 4 1 10 Start Failed Closes the TCP connection and the reference to the experiment module VI 1f an error occ
103. red traces on the hard disk of the PXI controller if the user wants to save the acquired traces without having them transferred to the host computer Synaptic Gain vi first builds paths to the template files and provides LoadTemplates vi with an array of SGLs containing the factors for scaling the templates Page 47 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide Next the template length number of data points is determined and memory for the template is allocated by initializing a 2 D array of SGLs An EOF is used to determine the file length bytes divided by 4 Subtracting the length of the header 128 SGLs 512 bytes em ral oa gives the template length as number of data points The template length is next divided by 5120 using Quotient amp Remainder because the template is going to be read from file and stored in the 2 D array in chunks of 5120 data points If the remainder 0 row size of the 2 D array is set to the integer quotient otherwise to integer quotient 1 This number is also fed into LoadTemplates vi together with the remainder giving the number of elements in the last data chunk and the header length in bytes of the template file 7 2 1 LoadTemplates vi The outer large For Loop in LoadTemplates vi executes once for each template file to read Its number of iterations is obtained by auto indexing the 1 D arrays ScalingFactors and TemplateFilePaths It
104. res a 1 D array of SGL at its scaled data input To transform the single command value calculated in the loop into the required 1 D array without invoking the memory manager a pre allocated by feeding a constant into the While Loop 1 D array of SGL with only 1 element is used and a Replace Array Subset to exchange the constant value with the calculated command value Because the opcode input of AO Single Update vi is set to output amp update AO Single Update vi sets the analog output channel to the new command value immediately after having received the 1 D array Thus the delay between acquiring the membrane potential analog input and giving the adjusted current command analog output depends only on the time it takes to perform the necessary calculations and consequently varies depending on the combination of virtual conductances used It 1s possible to fix the time interval between analog input and analog output by tying AO Single Update vi to the scan clock that controls the analog to digital conversions This is done by replacing AI Config vi and AO Config vi with AI control config vi and AO control config vi respectively The main difference is that AI control config vi has the ability to route signals By default it routes the AI scan start signal onto PFI7 AO control config vi has the ability to choose a clock source and specification By default 1t chooses PFI pin as a 3 For a description of V dependent Conduc
105. ta queue but also by receiving an abort command by the user This speeds up the Stop process new An analogous change has been made in Embedded llb IV Relation vi and Embedded llb V clamp vi G clamp llb G clamp vi The time out value for the event structure in the default case Check Controls has been made dependent on the Boolean variable DAQ in process and whether the queue determining the next case to execute is empty or not Thus as before if no data acquisition is in progress and the queue does not contain elements already the event structure times out after 250 ms Otherwise the time out value is 1 ms G clamp llb G clamp vi Using the Stop F12 button to abort an ongoing experiment now disables the button to prevent repetitive usage of the button as it can take some time before the effect of the abort command becomes apparent The button is re enabled after the stop of the experiment module on the PXI controller has been detected 01 22 2004 G clamp v1 1 2 Embedded llb ScriptAnalyzer vi The main script analyzing algorithm has been re structured to make its logic simpler While this revision does not affect functionality of ScriptAnalyzer vi 1t should facilitate future additions to the script language G clamp llb G clamp vi The calculation of the leak resistance has been moved in a new case of the Event Structure The calculation is triggered by a mouse up event in the graph on the IV Relati
106. tances vi see section 9 1 of the G clamp User Manual These VIs can be found in the library RT Control llb that should be located in your Lab VIEW 6 1 examples real time directory Page 41 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide clock source and 7 as the clock source specification The result is that the analog input scan clock is used to clock the analog output updates when the opcode input of AO Single Update vi is set to Output only This assures that each time a digital to analog conversion 1s clocked in the analog output is clocked out Note that AI control config vi includes AI start vi and therefore the call to AI control config vi should be the last operation performed in Sub vi before G clamp DQA vi is called to prevent overflow of the onboard FIFO After the analog output operation the Code Interface Node makes an assembly call to read the Time Stamp Counter register off the Pentium class processor and to obtain a time stamp with a resolution at the frequency of the PXI controller s CPU see section 10 2 The time stamp is stored in a pre allocated array for analysis after the While Loop has finished executing The execution order AO Single Update vi Code Interface Node is achieved by placing the Code Interface Node into a Sequence Structure and by wiring an output of AO Single Update vi to it thus forcing the Sequence Structure to wait until the output of AO Single Update vi is avai
107. te file with read esyn vi in Gsyn Threshold Sub vi or interprets the script with ScriptAnalyzer vi in V clamp Sub vi 4 calls the RT feedback loop module G clamp DQA vi to perform a data acquisition iteration Page 35 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 5 puts together the acquired traces with a header and adds it to the Result Data Queue so that the communication loop can send it via the TCP connection to the host computer As IV Relation vi is designed to perform a series of data acquisitions iterations tasks 3 4 and 5 from the list above are done repetitively in a While Loop while tasks 1 and 2 need to be done only once before the While Loop starts 10 00 0 00 E al z o Ol E dla 0 00 0 00 E S 0 00 0 00 IE Pale i E hi f T al Control Wakes j i iar al 1 oa gE a Mi 1 IV Relation Sub vi first performs a read on the queue Control Values to obtain the settings for the experiment Based on these settings a l D array of SGLs is initialized to pre allocate memory for the current trace passed into the While Loop and on to the Template Im Buffer input of G clamp DQA vi Pre opm0m000000 allocation of memory for the voltage PFP FPFF 0 Ce ee ee Page 36 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide trace is done in the While Loop in Build AO waveform vi a1 D array of cluster of 2 elemen
108. ter use in other cases the PXI target information is bundled into the corresponding cluster element of the large cluster that is passed from one iteration of the outer While Loop to the next via the top shift register 2 The IP address of the PXI controller obtained in the previous step is now used to establish a connection to the VI server of the LabVIEW RT Engine on the PXI For why that information is available in the control PXI Target see section 8 5 TargetList VI Page 9 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide controller using an Open Application Reference This reference enables Open VI Reference to obtain a reference to Embedded Ilb List Templates vi and to execute List Templates vi by invoking the method Run VI After List Templates vi has stopped G clamp vi invokes the method Get Control Value on the controls Available templates and Virtual G s of List Templates vi Finally the VI reference to List Templates vi is closed Any errors that might occur during this process are reported by Simple Error Handler vi r kW Status a Available templates Status i IS OO pe A as ll Res 1 A EE Getting list of template Files and conductances note H al m t 3 Get list of available template files and conductances So 11 dert WI e EE E 2555757575777 1 1 1 1 Get Control values Get Control Value TH Wait until done t Control Mame t Control Mame
109. tly into the While Loop of V clamp Sub vi that executes once per data acquisition iteration The simplification consists of stripping the feedback loop of any elements involved in the calculation of current through virtual conductances as virtual conductances are not used in voltage clamp In addition V clamp Sub vi contains all configuration VIs required to tie the output of the command signal by AO Single Update vi to the scan clock However because the opcode input of AO Single Update vi is set to output and update these settings are ignored and output of the command signal occurs as soon as AO Single Update vi executes Page 55 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide 8 Other custom VIs 8 1 AnalogInOutConfig VI AnalogInOutConfig vi contains two cluster controls that specify the settings for the analog input AI Cluster and analog out channels AO Cluster Execution of AnalogInOutConfig vi follows the same logic as outlined for TargetList vi section 8 5 It waits until the user is finished and then updates the output cluster indicators AI Cluster and AO Cluster from which G clamp vi derives the updated channel information when AnalogInOutConfig vi is called by the user via the menu File gt Preferences gt DAQ Board Configuration As with TargetList vi G clamp vi will invoke the method Make Current Values Default and subsequently Save VI This will make
110. ts U 32 U 32 is set up for the time stamps obtained during each cycle of the real time feedback loop from which later the RT loop info is determined the RT FIFO Result Data Queue is set up The 2 D array of SGLs contains initial values for the state variables of the activation and inactivation gates of the implemented virtual conductances This array is fed into the While Loop via a shift register Thus the first call of G clamp DQA vi starts with the state variables at arbitrary values and it will take some time before the state variables settle to normal values At the end of each data acquisition the last values of the state variables are put out from G clamp DQA vi into the shift register of the While Loop and used as the starting values for the next call of G clamp DQA vi Note also that the 2 D array is initialized with only 6 rows If more than 6 virtual conductances are implemented in V dependent Conductances vi another row has to be added for each additional conductance Otherwise the retrieval operation in V dependent Conductances vi will return Not a number and unpredictable results can happen 2 The analog input and analog output hardware is set up once outside the While Loop with AI Config vi and AO Config vi DAQ Hardware Settings vi provides the required parameters by translating the variants AI Cluster and AO Cluster into the appropriate data types AI Config vi and AO Config vi provide t
111. ub vi which is also an array of 4 elements 1s converted to a string and communicated to G clamp vi With these two TCP Write operations of Synaptic Gain vi G clamp vi completes execution of the New Data case of its Case Structure and proceeds to the Process case see section 4 1 11 3 Synaptic Gain vi next waits for 25 seconds for a TCP communication from V clamp vi the unwired timeout ms input of TCP Read defaults to 25000 The corresponding TCP Write of G clamp vi occurs in frame 0 of the Sequence Structure in the case processing Synaptic Gain data and indicates whether the user Page 51 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide wants the traces transferred to the host computer for display and whether he wants the traces saved by writing them to disk on the PXI controller see section 4 1 13 This communication is expected to be 2 bytes long and after arrival is converted to a 1 D array of Booleans The array is indexed and interpreted with Equal To 0 If the second array element is TRUE Synaptic Gain vi saves the traces into a file It first executes Write to Disk mod vi which creates the data file and writes the header 7 2 3 Write to Disk mod vi Write to Disk mod vi checks with File Directory Info whether a data directory Ini g clampidata dar already exists and if not it creates 1t with New Directory It formats the recording time Lia from a number secon
112. ules Embedded llb also contains a set of standard and custom VIs that are required as sub VIs In the standard LabVIEW RT architecture as advertised by National Instruments the host computer acts only as a graphical interface for program development and as the display of the VI front panel For program execution the code 1s automatically downloaded to the embedded processor While this arrangement works well it constrains performance because some of the memory and other resources available on the embedded processor must be dedicated to supplying display information to the host In order to maximize the embedded resources available for data collection and storage we employed an alternative programming method that involves LabVIEW being targeted to the host computer as opposed to the embedded processor With LabVIEW targeted to the host computer the G clamp vi running on the host acts as a client that uses the VI server of the LabVIEW RT Engine on the embedded computer to start and execute experiment module VIs Compare Chapter 3 Software Overview Programming LabVIEW RT Using the RT Development System with Communicating Using Host LabVIEW Applications in the LabVIEW Real Time User Manual Page 6 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide In general experiment module VIs are organized to perform two tasks in parallel for details and exceptions see the individual descriptions of the experiment modules ex
113. urred in the Start ExpModule Step2 case 4 1 11 New Data Uses the first TCP Read to check whether data are available on the TCP connection If nothing 1s sent via the TCP connection 7CP Read times out after 1000 ms and the error status of the error out cluster of TCP Read is TRUE The empty TRUE case of the large Case Structure executes and in the TRUE case of the small Case Structure the error code 1s analyzed Error code 66 indicates that the TCP connection was closed by the peer 1 e the experiment module VI As the experiment module VIs close the TCP connection only after they have finished transmitting data to G clamp vi error 66 indicates that the data acquisition is over the experiment module VI has stopped and the Stop case of G clamp vi should be executed next If the error code is not 66 1t is assumed that TCP Read simply timed out 1 e the experiment module VI is running but not sending data right now In this case the Check Controls case will execute next Thus during an experiment it takes up to 1000 ms before G clamp vi reacts to a user interaction on the front panel Because of the TRUE status of the variable DAQ in process after handling the user events execution will return to the New Data case as long as the TCP connection is open Page 22 of 88 Kullmann and Horn 2004b G clamp Programmer s Guide read data string size ET TEF e E aa a code If data
114. y after the Case as m AA Structure for saving the data has completed does the other Case Structure for transmitting the data to G clamp vi start executing It transmits each trace starting with the voltage trace by first transmitting a number a long integer I 32 converted to a string therefore 4 bytes indicating how many chunks of 5120 data points it will send before repetitively using TCP Write to transmit one 5120 data points chunk at a time 73 V clamp V clamp vi is essentially a clone of IV Relation vi The only difference is that the number of data acquisitions iterations to be performed is not derived from the variant DAQ Control Values but from the variant Script Script is first converted to a ead OOOO flattened string and with an Unflatten Script From String the script as seen on the front panel of G clamp vi 1s obtained 0 2 0 9 2 The reason for the sequential File I O and TCP IP is that we thought parallel execution might require duplication of the trace arrays Theoretically this should not be the case as neither operation changes the data and therefore LabVIEW should be able to use one copy of the data for both operations We suspect that something else might reduce memory requirement and especially speed up these operations According to a web presentation Handling large data sets in LabVIEW given by an NI engineer Damien Gray and the accompanyi

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