OmniLab Manual - Igor Kagan website
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1. Columns 1 6 A B readl X 1 reall Y 1 read2 X 2 real IV OmniLab Exported Binary File Format see also readbin m 2 X 2 OmniLab Manual 34 oe oo long integer oe 4 bytes single precision float 4 bytes oe Files have following simple structure oe Header oo o oe oe start time 8 chars oe comment length long oo oo oo NOTE oe Labview stores numeric data in Big number of channels long integer number of scans long integer Scan rate Hz single precision float integer comments comment length chars Data single precision floats Endian Form most significant byte first Other applications typically expect numeric data to be oo oe oo function MACHINEFORMAT that in little endian form files should be transformed to Little should be used for these files least significant byte first See help fopen for files oe In this case Endian Form before using by these applications In Matlab 5 x there is a parameter in FOPEN ieee be or b IEEE floating point with big endian byte ordering more details on how to read big and little endian OmniLab Manual 35 OmniLab ASCII File Format Number of scans x Number of channels delimited by TAB E2. ra Output triggers for communication Variable sampling rate Switch between monitoring and record modes Log the entire experiment to separate file with decimated sampling rate Streaming to disk capabilities m Calibration routine Various display options E Online data analysis during data acguisition SE A fu m JA n 3 l i ON Mark events in data with time stamped NANA MUU Ju n j E comments N NN IN NAR E B Full screen mode is as ze cs os vo we o ID eo es sp Playback mode Retrieval and analysis of data blocks according to event comments Export data regions of interest or whole blocks to System Req u i rements ASCII or binary file Sample Matlab software and source code 586 PC National Instruments data acquisition DAQ board with NI DAQ drivers available for reading and analysis of Windows 2000 NT Me 9x with minimum 32 MB RAM 128 MB recommended exported binary files Overview OmniLab is a versatile data acquisition and analysis software package designed specifically for physiological labs OmniLab is written in LabVIEW National Instruments http www ni com and works with NI DAQ hardware While OmniLab basic package already includes many features and options powerful LabVIEW programming environment and flexible modular structure of OmniLab allow quick and efficient customization and tailoring for even more specific customer
3. Note You should upgrade BEFORE you run OmniLab for the first time To install upgrade patch complete the following steps Installing upgrade from NI website 1 Download the setup exe file for your specific language version of LabVIEW from NI website http www ni com search for LabVIEW 6 0 2 upgrade 2 If you have the LabVIEW Professional Development System or you have purchased the LabVIEW Application Builder separately then you should also download the LabVIEW Run Time Engine 6 0 2 installer 1vrt msi for your specific language version of OmniLab Manual 18 LabVIEW and copy it to the LabVIEW 6 gt applibs installs directory where you must replace the file with the same name that already exists in that location 3 Make sure LabVIEW is not running 4 Run setup exe by double clicking on the file or select Run from the Windows Start menu and type x setup in the input box where x is the full path to the directory where the downloaded file is located e g be c Windows Ntemp Note Choose Mass Compile option when prompted 5 Now you can start OmniLab Installing upgrade from OmniLab CD 1 Make sure LabVIEW is not running 2 Run the setup exe from 60 0 2 directory by double clicking on the file x N6 0 2Nsetup exe or select Run from the Windows Start menu and type x 6 0 2 setup in the input box where x is the letter of your CD drive Note Choose Mass Compile option when prompte
4. Select Calibrate channels in the main menu Press Run In Calibrate Channels OmniLab Manual 49 Select channel Press Acquire for the Ist point lower lim while supplying the appropriate known signal Type real world value for the 1st point e g 0 mmHg and press button 1 Press Acquire for the 2nd point upper lim while supplying the appropriate known signal Type real world value for the 2nd point e g 100 mmHg and press button 2 Repeat for each channel that you want to calibrate Press Create Cal Matrix Press Save Cal File Press Done 1 1 2 To append change previously saved calibration Select Calibrate channels Press Run Press Load Cal File choose previously created cal file and use procedure 1 1 1 starting from the step Select Channel for each channel that you want to update Note if you performed Calibrate Channels step before starting the Acquisition and did not exit OmniLab the created calibration is valid and will be applied to the datafile automatically In this case you do not need to perform the Load Cal File step in Acquisition setup see below 1 2 Acquisition setup Select Acquisition setup in the main menu Press Run 1 2 1 Basic options Choose channels separated by comma 0 15 e g 1 2 OmniLab Manual 50 1 2 2 Choose scan sampling rate default 1000 or 200 Hz Optional Load calibration press Load Cal
5. freeze chart F7 file info save file info in text file F8 Print with comments save chart save chart to graphic BMP format 3 1 3 Navigate along the file Select required block s according to user comments and time and press SHOW BLOCKS F4 or F4 3 1 4 Move along selected block s Manual change scroll t2read and t scale Auto use Play Stop and Rewind Stop buttons during Rewind the autoscale will be on The velocity of Play Rewind is set by t2read and maxvel controls See Help on maxvel for more info 3 2 _ Data export Buttons Save ASCII Save bin export the data that is currently displayed on the chart OmniLab Manual 57 Save Blocks will export selected block s to binary format Press split blocks if you want to export each block to a different separate file 4 Analysis 41 Analysis setup Select Analysis setup in the main menu Press Run Note Currently only smoothing filter is available Select channel from Channels menu and set Smoothing and Sigma Sigma in seconds is the parameter of Gaussian bell that will be convoluted with the channel signal to smooth it The more is the Sigma the wider is the Gaussian bell the smoother is the signal Note the Analysis setup option works also during the Display mode you do not have to stop and call Analysis setup each time you have to change Analysis settings However you have to press SHOW B
6. 35 55 2 o notitiam opt bord a IRR 26 Monitoring scope mode iei eter rere cette Ee A E REPE waw IRE ee an T ATA E Re peor enne 26 Recording mode it et ptite ree er abra e EO rt be e DE 26 CHAPTER 4 RETRIEVING DATA 27 CHAPTER 5 EXPORTING DAT TA 27 CHAPTER 6 PRINTING DATA seen ense Swasta qanuna as 27 CHAPTER 7 HELP AND TROUBLESHOOTING 28 HEEB annua E a m RE Cetus nOD aU en deter IA 28 TROUBLESHOOTING IHE edeuveguesoetensencearentsecdues 28 APPENDIX A OMNILAB DATAFILE FORMAT A 29 APPENDIX B CHANGES 0 ccsscsscsscsscscssscsssnssscsnssesssscesssssnssesenessssnescessessnssessnessesessnesessnessese us kisa 37 APPENDIX C EXAMPLES 43 APPENDIX D README FILE 44 KEY NAVIGATION SHORTCUTS u maa 45 OmniLab Manual 6 APPENDIX E SAMPLE MATLAB M EILES
7. 46 READBIN M c oett mate masma Hale io Es tasted acs eem s latius ost kaba 46 APPENDIX F QUICK REFERENCE GETTING STARTED INSTRUCTIONS 48 GENERAL INSTRUCTIONS adiret ite eto t Pe P Re teach seis awas suhe Xa Guedes uu a uya 48 Saving default values i ie ee yere eR edt e S ee Rap eee e t e a de 49 START issver sut Sma QH kawana au ua suqu a sua m Q uka aaa upaya 49 1 SETUP M HO 49 IL Calibration sso du NR RE RR e Cah E n ge di 49 1 2 ACguisiltonsselupauxsa suse aeree ope E p e ped pe ces 50 I3 Online processing set p en ri Ua d TUR Ea 51 2 ACQUIRE MODE ONLINE MONITORING AND RECORDING enne ener entere nnne nnn 52 21 P 53 22 Recordi MEE q u AA BBR PBR eb Hak Sul aue tee ok wee aU 55 3 DISPLAY MODE DATA RETRIEVAL AND EXPORT enne entere entrer entere rennen nenne enne 55 34 Data retrievdlc sai e ee a e 56 3 27 D ta exportca ssim we eate e e e DG E He ER RA sedans 57 4 ANALYSIS Go eon n DPI p EORR OM t EP RES 58 44 JAhalysis setup suia ee i ER RE E ER NER RR ER EE REI aS unus 58 42 Cursor graph ee e rre a e PR ep te prete P PUR cds i pareat 58 43 Heartt te estimation uie d a OR ERR E ED NR HERR UR sis EM ER IEEE unas 58 5 DISPLAY BIN LOG pio ERRORI OBERE Dr t UIS 58 6 PRINTING S sh aga nen mi aenea o iara ES 59 6 1 D
8. Decimation of large segments 210 000 points of data before presenting them on the Screen Please let me know what features you would like to see in future releases OmniLab Manual 15 Chapter 2 Setting Up Your System This chapter explains how to set up your OmniLab system and start the OmniLab application Minimum System Requirements Your computer must have the following hardware and software to work with OmniLab Microsoft Windows 95 98 NT 2000 Windows 2000 1s recommended PC with Pentium 586 processor or higher CD ROM drive or floppy drive or Internet connection VGA resolution or higher video adapter Minimum of 32 MB of RAM 128 MB recommended At least 25 MB free hard disk space Microsoft compatible mouse NI DAQ software and DAQ hardware see below LabVIEW 6 0 2 or LabVIEW 6 0 2 Run Time Engine see below Installing Your NI DAQ Software To install your NI DAQ software refer to the NI DAQ User Manual for PC Compatibles When you install NI DAQ use the Driver Files Installation option which is the default setting OmniLab Manual 16 Installing Your Hardware To install and configure your hardware refer to the user manual for your National Instruments data acquisition DAQ hardware Installing LabVIEW If you use LabVIEW based OmniLab version you will need to install LabVIEW software To install LabVIEW refer to the your LabVIEW documentation package If you
9. File and choose previously created cal file You typically will perform this step if you want to use old calibration Choose scan sampling rate in Hz per each channel default 200 or 1000 Enter general comments up to 1900 characters You may also enter general comments later Select block record duration s to record blocks of a predefined duration or leave it 0 if you do not want automatic stop record Log file on off choose on for this option if you want to log save the entire experiment i e also when in Scope and not only in Record mode default off Log rate sampling rate of log file default 100 Hz Advanced options Press in expand hide options to set advanced options Buffer size scans samples set the buffer size for buffered acquisition 1 3 Online processing setup see also OnlineProcessing txt 1 3 1 Select Online processing from the main menu Press Run Pressure Select pressure channel low pass cutoff for low pass filter and filter order default 1 none 25 Hz and 10 Pressure channel will be used for dP dt which will be displayed as channel 15 last channel in chart legend OmniLab Manual 51 If no dP dt is needed select 1 for pressure channel 1 3 2 Heart rate Select ECG channel and analysis mode default 1 none and via spectrum The selected ECG channel will be used for heart rate estimation If no heart rate is needed select 1
10. change to Do not change file if you are going to continue working with the same file 3 1 _ Data retrieval Select block or number of successive blocks to read in Block Comments select all will select all blocks in file Press SHOW BLOCKS F4 or F4 to read and show selected block s scroll sets the offset from the beginning of data block s selected seconds dur shows the duration of data block s selected seconds 3 1 1 Chart options t2read time that is shown read from the file see also Play t scale s time scale default 10 seconds xgrid s time scale division default 0 5 seconds grid on of default on grid color default light grey y split arbitrary vertical offset between channels default 0 xautoscale when on t scale will be equal to t2read all y auto all plots panels autoscale on off below are y autoscale on off individual controls according to number of plots panels plots change F5 or F5 change chart options press after entering new settings Channel settings Any channel can be put on any panel plot select appropriate plot next to the channel LED Change color for each channel OmniLab Manual 56 select appropriate color next to the channel LED Show sel show selected channels show LED is on Show all Hide all You have to press SHOW BLOCKS F4 or F4 to bring new channel settings to effect 3 1 2 Additional options F6
11. description of terms used in this manual including abbreviations and acronyms The OmniLab datasheet OmniLab Manual 11 Conventions Used in This Manual The following conventions are used in this manual lt gt bold bold italic italic courier Angle brackets enclose the name of a key on the keyboard for example lt Shift gt A hyphen between two or more key names enclosed in angle brackets denotes that you should simultaneously press the named keys for example lt Ctrl Alt Delete gt The symbol leads you through nested menu items and dialog box options to a final action The sequence Operate Change to Edit Mode directs you to pull down the Operate menu and select the Change to Edit Mode item Bold text denotes the names of menus menu items buttons and other controls and indicators Usually names in inverted commas Bold italic text denotes a note caution or warning Italic text denotes variables emphasis a cross reference or an introduction to a key concept Text in this font denotes text or characters that you should literally enter from the keyboard sections of code programming examples and syntax examples This font also is used for the proper names of disk drives paths directories programs subprograms subroutines device names filenames and extensions and for statements and comments taken from programs OmniLab Manual 12 courier bold Bo
12. for ECG channel Note This part will be revised in the next release 2 Acquire mode online monitoring and recording Create new folder in C Data e g test200501 using for example Windows Explorer Click Explorer shortcut double click My Computer Local Disk C Data then press File New Folder type folder name and press Enter Select Acquire data in the main menu Press Run Select file name default experiment name date e g test200501 dat and save it to the created folder In dialog Save as double click folder Data then created folder and press Save Date format ddmmyy day month year Notes 1 If no calibration has been applied warning No calibration applied will appear Press Continue if you want to continue working without calibration or Stop if you do want to apply calibration 2 Acquire data mode will run only after you performed valid Acquisition setup If you want to append new data to the existing datafile select Do not change file option OmniLab Manual 92 If you do not have any datafile open that is you are just starting working you can select datafile from the disk and append new data to it If you already have open datafile new data will be appended to it without asking you any more questions this is useful when you for example stopped the acquisition went to Display mode to review the file and now want to continue recording new block
13. polarity scale multiplier and scale offset parameters are required to reconstruct data waveforms 4 Data 2D array each column one channel each row one scan WOW WOW WoW WoW Wow Wow Wow S wo Uo Wo Wow oy so won won Wow Won wow ow ScO ch0 ScO ch1 scO ch2 WOW WOW WoW Wo Wow Wow Wow Wow Wow W oy W oy Won WoW WoW ow ow ow own Wow oq Scl ch0 Scl chl scl ch2 WOW WOW WoW Wow Wow 5 bytes chars Byte stream written to file contains data in the following manner Header scan 0 channels scan 1 3 LabVIEW stores numeric data in Big byte first in little endian form files should be transformed to Little these applications ENDIAN and LITTLE Examples of BIG Endian Form least significant byte first channels ec o Rv most significant Other applications typically expect numeric data to be In this case Endian Form before using in ENDIAN formats OmniLab Manual 33 2 bytes integer 1 LabVIEW hex form 00 01 Matlab hex form 01 00 4 bytes single float 2 5 LabVIEW hex form 40 20 00 00 Matlab hex form 00 00 20 40 II OmniLab Log File Format Same as Exported Binary File TES OmniLab Cal File Format Calibration Y AX B ASCII TXT file Number of channels rows 16 x 6 columns delimited by TAB
14. that displays the data Consist of one or more panels plots An item on OmniLab front panel user interface that can be changed by user e g button OmniLab Manual 60 D DAQ DAQ hardware datafile decimation device display mode event F front panel G CUI Data acquisition The equipment that takes the data from physiological monitoring devices sensors and transfers the data into your computer File recorded to disk during the Record mode contains one or more data blocks Process of reducing a large set of data values to a smaller more manageable size During data acquisition decimation can be achieved by re sampling the data with lower sampling rate OmniLab uses this technique when the user requests to log the entire experiment to decimated og file The instrument that measures and collects the data DAQ board Data retrieval analysis and export mode Works with previously acquired datafiles Continuous data segment recorded to file and marked by time stamp and user comment Also called block A part of VI visible to the user graphic user interface GUI Graphic user interface OmniLab Manual 61 Hz I indicator LED log file M monitoring mode NI DAQ Hertz samples or scans per second An item on OmniLab front panel user interface that displays information and can not be changed by the user Light emitting diode Omni
15. you load calibration the message confirming this action will appear for example OmniLab Manual 24 Calibration file loaded C Igor OmniLab cal151100 cal Enter general comments up to 1900 characters You may also enter general comments later via Info dialog see Chapter 4 Retrieving Data Set block record duration in seconds to record blocks of a predefined duration and automatically stop an acquisition after the specified time elapses Leave it 0 if you want manual stop of recording Set log file on off choose on for this option if you want to log save the entire experiment i e also when in Scope and not only in Record mode default is off Set log rate sampling rate of the log file default 100 Hz Advanced options Press in expand hide options to set advanced options Be absolutely sure you understand these setting before changing them The buffer size in scans or samples set the buffer size for buffered acquisition In slow systems with little RAM e g 500 MHz CPU 32 MB to optimize performance write 0 5 to 1 seconds worth of data to the file therefore set scans2read see Acquire data mode below to scan rate or scan rate 2 Then set buffer size to at least 1 5 times scans2read In fast systems with lots of memory you can leave the buffer size big enough but use much smaller scans2read values to achieve smooth update of fresh data on the chart see Acquire data mo
16. ING LABVIEW aiite ret ree eee e SS ee eee SSS 17 INSTADEING OMNILAB nonor siirad tiitel CR EY CEDE e E ERE e A Eee sS 17 Installing from OmniLab CD e e e eite nte ne e rege Ure cv eee e 17 OmniLab Manual 5 Installing from OmniLab floppy diskettes esses eese etre 18 Installing from OmniLab website eren rennen entente trennen 18 UPGRADING TO LABVIEW 6 0 2 FROM 6 0 o cccccccceccsseessesecssesscssesscsscesessessuesecseesscsessessesessecsuesscsessseneeseengs 18 Installing upgrade from NI website eese eene enne ettet tne tren trennen 18 Installing upgrade from OmniLab CD sees ene etre ener tnter trennen trennen 19 STARTING OMNILAB 115350 ESL I open a eimi p OHIO os DERE RUE QR ITEM 20 CHAPTER 3 ACQUIRING DATA MONITORING AND RECORDING 21 CALIBRATION sS gk saa anqana aysana qampata naska nn Oh E 21 Cr te New Callbratiohiu gan e RR EE e op ae Rete umala usss 21 Update Old Calibration ee tea ri e dots cane 23 Change Calibration in Datafile de east ari chen derit i a e eei 23 A COUISITIONISETUP hua n E saus that rre D e eli ea DIR nS 23 B sic ODIOhss iss a Ja RH re usus 24 Advanced OPHONS usq n eR E EUR ERE RI REOR e ee rere CHEER ha Sl ss 25 ACOUIRE DATAMODE
17. LOCKS F4 or F4 to bring new analysis settings to effect 4 2 Cursor graph Will be modified and documented later 4 3 Heart rate estimation Will be modified and documented later 5 Display bin log Will be modified and documented later OmniLab Manual 58 6 Printing 6 1 Display and Acquisition modes Ctrl F8 or File Print Window Ctrl P print visible Window Use Esc to put chart in Full Screen mode 6 2 Display mode Print F8 use to print chart only there are options to add Notes Axes labels save to HTML and PNG etc Custom Print Settings Edit Preferences Printing OmniLab Manual 59 Glossary A acquisition of data acquire mode B block of data C calibration cal file channel chart control Recording data to computer memory for display and or to file for storage Data acquisition mode includes Record and Monitoring Scope mode Continuous data segment recorded to file and marked by time stamp and user comment Also called event Procedure that links voltage data with real world physical value Performed for each channel sensor separately Calibration file A pathway between data acquisition hardware and computer Each sensor transducer output DAC input signal is connected to one channel Channels are labeled ACHO ACHI and so on on your terminal connectors such as the BNC 2090 and BNC 2091 and 0 1 15 in OmniLab interface The chart
18. Lab uses a virtual LEDs in its user interface as indicators File recorded to disk and containing the entire experiment usually uses smaller than datafile decimated sampling rate Mode that includes data acquisition and display of the acquired data on the chart Different from the recording mode Also called Scope mode National Instruments data acquisition driver software OmniLab uses this software to communicate with your DAQ hardware OmniLab Manual 62 panel path plot R recording mode scan rate sampling rate scope mode T view Panel on multiple panel chart when Stack Plots option is on and plots is more than one Also called plot Can contain one or more channels All channels in the panel share the same Y axis Y scale Directory folder where OmniLab will create various files See panel Mode that includes data acquisition display on the chart and writing saving the acquired data to the file Different from the monitoring scope mode See sampling rate Number of data points per one second worth of data also called scan rate See monitoring mode User interface window GUI front panel OmniLab Manual 63 OmniLab Manual 64 OmniLab datasheet Please see the next page OmniLab Datasheet 65 OmniLab Physiological Data Acquisition Retrieval and Analysis Features z a a ET E 77 EET ari Koji J 4 Up to 16 analog input channels
19. Omni Lab OmniLab Manual January 2002 Edition Copyright 2002 Igor Kagan All rights reserved Support For support please contact Igor Kagan Email kigorQ tx technion ac il Website http igoresha virtualave net Lab VIEW OmniLab OmniLab Manual Important Information WARNING REGARDING MEDICAL AND CLINICAL USE National Instruments products are not designed with components and testing for a level of reliability suitable for use in treatment and diagnosis of humans or as critical components in any life support systems whose failure to perform can reasonably be expected to cause significant injury to a human Applications of National Instruments products involving medical or clinical treatment can create a potential for death or bodily injury caused by product failure or by errors on the part of the user or application designer Any use or application of National Instruments products for or involving medical or clinical treatment must be performed by properly trained and qualified medical personnel and all traditional medical safeguards equipment and procedures that are appropriate in the particular situation to prevent serious injury or death should always continue to be used when National Instruments products are being used National Instruments products are NOT intended to be a substitute for any form of established process procedure or equipment used to monitor or safeguard human health and safety in medical or
20. Save Blocks functionality to Display mode Added All select all blocks button to Display mode 30 11 00 Added Block Comments History to Info in Acquisition mode Abort Button and Run Continuous Button removed 26 11 00 Added Start Path functionality to Display mode Cosmetic changes Warning about No Calibration added to Acquisition mode OmniLab Manual 41 OmniLab v 1 0 c Early development OmniLab v 1 0 b changes not documented first version OmniLab Manual 42 Appendix C Examples This section will be available in the next edition of the Manual not documented yet OmniLab Manual 43 Appendix D ReadMe File OmniLab README Updated 02 01 02 This folder contains source code for OmniLab software written in Labview 5 1 1 G Programming Language and converted to 6 0 2 version OmniLab version 4 0 for MS Windows 95 98 NT 2000 written by Igor Kagan http igoresha virtualave net LabVIEW OmniLab html Copyright c 1999 2002 Igor Kagan All Rights Reserved See License txt for more information kigor tx technion ac il Dept of Biomedical Eng Technion IIT Haifa 32000 Israel OmniLab Manual 44 See also OmniLab Help file OmniLabHelp chm Format txt Calibration txt Changes txt Acquisition txt Instructions txt readbin m readlvf m and OmniLab Manual Key Navigation k
21. TENTS irr de ipe h K i S kent dp ut Pede ire SA SASS 5 FIGURES ete ee ettet Bh Sees tne ex Sosa ioe tede ien dide 9 ABOUT THIS MANDJAL eiie eo bos vo sn ston essceveonecessonssicoseseasesusaucsdevessoseoussciiugtesvssestestevesdadesneds oovsuececeesos 10 ORGANIZATION OF THIS MANUAL uu u I a 10 CONVENTIONS USED IN THIS MANUAL cccccccccccccccsecesescsesecesesesesesesesesesssesesesesesesesesesesesssesssssssssesssseseseseseaes 12 CHAPTER 1 INTRODUCTION TO OMNILALJ 14 WHATIS OMNILDADB fce e e etre decem ee ee ee ree Pete ceded eee rede de SQ u Qu ert 14 OMNILAB FEATURES u u I iet echec eee eec t ee e e n e hp re uqa dass 14 FUTURE DEVELOPMENT PLANS nana nu 15 Current Fo DO USE s in nunata od ete edo coe oct apio de oe taa dad cte ced bc 15 CHAPTER 2 SETTING UP YOUR SYSTELM 16 MINIMUM SYSTEM REQUIREMENTS scssccssccecsesessscecececeesesssaeceeccecsesssaeceeececseseaaececececseneaasaeceeeesesennsaeeeesesenes 16 INSTALLING YOUR NI DAQ SOFTWARE cccsssssceesessececsescecseaececsensececseeeecsesseeecsesaececsceeceesaeeecsesaeeeenesaeeess 16 INSTALLING YOUR HARDWARE rte eee FE EP a e abe E A EFE EET Re 17 INSTALL
22. ab version 3 and higher for MS Windows 95 98 NT 2000 written by Igor Kagan Copyright c 1999 2002 Igor Kagan All Rights Reserved kigor tx technion ac il Dept of Biomedical Eng Technion IIT Haifa 32000 Israel FILES CREATED BY OMNILAB Ls DataFile LI og File III Cal File IV Exported Binary File V Exported ASCII File OmniLab Manual FORMAT DESCRIPTION OmniLab DataFile Format LEGEND char 1 byte integer 2 bytes long integer 4 bytes single precision float 4 bytes DATA FILE STRUCTURE E Total Header gt User Header The data are stored in binary files using a following format UserHeader gt BlockComments gt Binary LabVIEW header gt DATA Total Header length 4 bytes long integer 0 3 User General Header length 4 bytes long integer 4 7 Number of 4 bytes long integer 8 11 Number of 1 2 bytes integer 12 13 Channels sA a S e ue 32 bytes array of two bytes integers 14 45 Scan rate frequency Hz 4 bytes single float 46 49 Date and Time Rue ae tae 50 bytes chars 50 99 Mer SOT rs ees a u NE erst e sue e E RS E ae al 40 bytes chars 100 139 OmniLab Manual 30 Calibration Coefficients a amp b 16 x bytes single floats 140 267 Gene
23. ach row one scan sample Each column one channel OmniLab Manual 36 Appendix B Changes OmniLab History of Development Changes Latest revisions go first Latest version 4 0 02 01 02 Record button RED when recording Logfile button moved XScale precision added when t ime scale 1 second two digits precision Acquisition Setup revised Analysis Setup added Smoothing option added to analysis Cosmetic changes Change Chart steps reordered now autoscale Y updates correctly after moving channels between plots 27 11 01 Major changes in graphics and UI one chart instead of many up to 8 plots panels channel color selection LabVIEW bug Crash when go to Full Mode with plots gt 1 and data in chart PrintChart F8 revised HTML PNG printing added Y axis label printing option added SaveChart to BMP added CursorGraph added Grid color added OmniLab Manual 37 OmniLab 4 0 201 Bug discovered gaps between successive portions of samples presentation only datafiles are OK Cosmetic changes T3 11 07 PrintChart changed Cancel button added Pop up windows changed to Modal In all pop up windows Cancel assigned to Escape and Done OK to Return Enter Cosmetic changes Maxvel control maximal velocity of playback added to Display mode 25 0 01 Digital line output added on StartRecord to trigger another compute
24. al and OmniLab software effectively you should be familiar with the Windows OS No programming knowledge is required Organization of This Manual This manual is organized as follows Chapter 1 Introduction to OmniLab introduces the OmniLab application Chapter 2 Setting Up Your System explains how to set up your OmniLab system and start the OmniLab application Chapter 3 Acquiring Data Monitoring and Recording gives instructions for acquiring data with OmniLab after you have set up your system Chapter 4 Retrieving Data explains the ways you can retrieve display and analyze data in OmniLab Chapter 5 Exporting Data explains how to export OmniLab data to other applications formats OmniLab Manual 10 Chapter 6 Printing Data explains how OmniLab can print snapshots of your data as they appear on the screen or print reports that summarize the data you acquire Chapter 7 Help and Troubleshooting explains how to use the OmniLab online help features and also offers some troubleshooting tips Appendix A OmniLab Datafile Format Appendix B Changes describes history of development changes Appendix C Examples gives you step by step examples on how you can use OmniLab Appendix D ReadMe file Appendix E Sample Matlab m files for reading OmniLab exported datafiles Appendix F Quick Reference Getting Started Instructions The Glossary contains an alphabetical list and
25. alibration that is currently in the memory after you created it in Calibrate channels or loaded it from Acquisition setup see later will be written to the header of this datafile However you can change the calibration in the existing datafile by pressing Change Cal in Data File and choosing the datafile you want to make changes to Acquisition setup Before you start acquiring data you have to perform Acquisition setup You need to do it each time you start restart OmniLab and are going to monitor record new data You will not be able to proceed to Acquire mode without having valid Acquisition Setup The system will display warning No channels selected Please go to Acquisition setup and stop OmniLab Manual 23 When you call Acquisition Setup mode the following view appears b AcquisitionSetup vi File Edit Operate Tools Browse Window Help 13pt Application Font ESI EPN LOAD CAL FILE nter general comments ere 88 I 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Figure 5 Acquisition setup Basic options The items required for valid setup are channels and scan rate sample rate Hz Button selects all channels Channels should be listed in ascending order and separated by commas Optional parameters Load calibration press Load Cal File and choose previously created cal file You typically will perform this step if you want to use old previously created and saved calibration When
26. clinical treatment National Instruments www ni com Since OmniLab is based on NI LabVIEW the above statement equally applies to the OmniLab software OmniLab Manual 3 License OmniLab copyright c 1999 2002 Igor Kagan All Rights Reserved LICENSE AGREEMENT You should carefully read the following terms and conditions before using this software Your use of this software indicates your acceptance of this license agreement and warranty One registered copy of OmniLab may be used by a single person lab on one or two computers at any time including portable or home computer Disclaimer of Warranty THIS SOFTWARE AND THE ACCOMPANYING FILES ARE SOLD AS IS AND WITHOUT WARRANTIES AS TO PERFORMANCE OR MERCHANTABILITY OR ANY OTHER WARRANTIES WHETHER EXPRESSED OR IMPLIED IN NO EVENT SHALL IGOR KAGAN BE LIABLE FOR DAMAGE OF ANY KIND LOSS OF DATA LOSS OF PROFITS BUSINESS INTERRUPTION OR OTHER PECUNIARY LOSS ARISING DIRECTLY OR INDIRECTLY THIS DISCLAIMER OF WARRANTY CONSTITUTES AN ESSENTIAL PART OF THE AGREEMENT Igor Kagan kigor Otx technion ac il http Agoresha virtualave net OmniLab Manual 4 Contents Table of Contents SUPPORT Su E 2 IMPORTANT INFORMATION 3 IB LG Ojo Po 4 GL OM UO M Lor 5 TABLE OE CON
27. d 3 If you have the LabVIEW Professional Development System or you have purchased the LabVIEW Application Builder separately then you should also copy the LabVIEW Run Time Engine 6 0 2 installer 1vrt msi tothe LabVIEW 6 gt applibs installs directory where you must replace the file with the same name that already exists in that location 4 Now you can start OmniLab OmniLab Manual 19 Starting OmniLab To start OmniLab select Start Programs OmniLabvx OmniLab vx where x is OmniLab version e g x is 4 0 or double click OmniLab vx shortcut on your desktop version 4 0 02 January 2002 Data Acquisition amp Retrieval Copyright c 1999 2002 by Igor Kagan Loading Figure 1 OmniLab splash screen When splash screen disappears you should see the main OmniLab window in the Acquire mode see below If window title bar looks like the sample bar below the name is without star and the Run arrow button look like the sample button below the arrow is not broken chanced are good that the installation succeeded gt OmniLab v 4 0 build 02 01 02 File Edit Operate Tools Browse Window Help Figure 2 OmniLab title bar and Run button OmniLab Manual 20 Chapter 3 Acquiring Data Monitoring and Recording This chapter gives instructions for acquiring data with OmniLab after you have set up your System Calibration The first thing you probably want to d
28. de below The device is the number of DAQ board usually 1 OmniLab Manual 25 Acquire data mode Monitoring scope mode Recording mode OmniLab Manual 26 Chapter 4 Retrieving Data Chapter 5 Exporting Data Chapter 6 Printing Data OmniLab Manual Chapter 7 Help and Troubleshooting This chapter explains how to use OmniLab Help options and gives some troubleshooting tips Help Press Ctrl H to bring up the Help Window for individual items controls and indicators You can also call this window by Help Show Context Help Place cursor over OmniLab icon upper left corner to see some essential information about this software Use Help Help For This VI to open Compiled HTML Help for OmniLab Troubleshooting This section contains some hints to help you with most frequent questions arising while using OmniLab Changes to chart options do not produce any visible effect If you are in Acquire or Display mode press change F5 or F5 button If you are in Display mode press SHOW BLOCKS F4 or F4 button to re load data to the chart Cannot see the data in a chart during Display mode Be sure that you have clicked on the SHOW BLOCKS F4 or F4 button Click on the Y auto scale checkbox besides the chart on the left OmniLab Manual 28 Appendix A OmniLab Datafile Format UPDATED 08 05 01 This file contains description of datafile formats created by OmniLab software OmniL
29. eing updated with these data on each press of the 1 or 2 button Of course you can come back and correct the entries if something went wrong Moreover you can enter data to the table manually if for some reason you have a need to do so 0 real value Message Window CREATE CAL MATRIX LOAD CAL FILE CHANGE CAL IN DATA FILE Figure 4 Control part of CalibrateChannels view Repeat this procedure for each channel that you want to calibrate Them press Create Cal Matrix and new calibration table will be created Now you can Save Cal File Press Done when you are done Now your calibration is saved in the cal file and OmniLab Manual 22 in the memory Last thing means that if you will start new datafile the created calibration will be used in this datafile The calibration will remain in the memory until you overwrite it with new calibration or exit OmniLab Note if you press Cancel instead of Done the cal file still will be created but no calibration will reside in the memory Update Old Calibration In the CalibrateChannels view press Load Cal File and repeat steps described in the previous section for each channel that you want to update fix Remember to press Create Cal Matrix before you save calibration to the file You can save it as new cal file or replace the existing one the one that you just loaded in Change Calibration in Datafile When you open a new datafile the c
30. experiment to separate file with decimated sampling rate streaming to disk capabilities convenient calibration routine separate calibration files various display options mark events in data with time stamped comments Data Display and Analysis Playback mode navigate datafile and retrieve data blocks according to event user comments various analysis options OmniLab Manual 14 Data Export Export data according to regions of interest whole blocks or entire datafile to ASCII or binary file for further analysis in other software applications sample Matlab software and source code available for reading and analysis of exported binary files Various printing options and saving charts to different graphics file formats Future Development Plans OmniLab is under continuous development and is constantly improving well I hope it is Most improvements are a direct result of customer feedback I welcome any suggestion for OmniLab development If you have any ideas requirements or bug reports please contact me by email at kigor tx technion ac il with subject OmniLab Thank you Current To Do list 1 Multiple profiles with options saved in INI file 2 Automatic restart after 640 MB limit stop during data acquisition 3 Automatic save to binary option during data acquisition 4 Ability of partition to blocks events segments during continuos acquisition i e without going to monitoring scope mode 5
31. eyboard shortcuts Escape F1 F2 F3 F4 F5 F6 7 F8 CErL E 8 Main window toggle between full normal chart graph screen stop start record select block comment field show selected blocks change chart options freeze chart info print chart print front panel Pop up windows Escape cancel close window and return to main window Enter Done OK OmniLab Manual 45 Appendix E Sample Matlab m files readbin m Example code for reading binary files created by LabVIEW OmniLab software Can be used to read log decimated files as well Copyright c 1999 2001 Igor Kagan 2 2 O 2 9 S 2 s S O 0 O S O S 9 O S O S O S S 9 O O O 9 O S s S O S S S O S O 9 O O O S O S S O 9 S O Q O oe oe long integer 4 bytes oe single precision float 4 bytes oe oe Files have following simple structure oe Header oe number of channels long integer oe number of scans long integer oe Scan rate Hz single precision float oe start time 8 chars oe comment length long integer oe comments comment length chars oe Data single precision floats oe NOTE oe Labview stores numeric da
32. fo revised Display mode revised Print chart added OmniLab 2 1 15 01 01 4 plot chart added to Display mode Graph version is still available in 1 20 362 Cosmetic changes Fixed FreeDiskSpace Checking Fixed Comment length from 32 to 31 User s 17 OmniLab 2 0 14 01 01 Formats of bin SaveBinary and SaveBlocks and log files have been matched Full Screen added to Acquisition mode X and Y grid fixed in Acquisition mode Decimated log file 100 Hz added to Acquisition mode 02 01 01 Comment length and Comment fields added to binary file header in Save Blocks Wait added to main loop in Display mode OmniLab Manual 40 Close x button disabled while running Split blocks save each block to separate file in batch mode added to Display Mode Append to empty file bug fixed 27 12 00 Time format chnaged to 24 hours Fl and F2 keys exchanged 20 12 00 Warning about insufficient disk space added to startup of Acquisition mode Check of free disk space added while recording data stop recording if less than 100 Mb remained Scroll max initialization to one added to Display Mode 18 12 00 Time Stamp in Block Comment changed to format hh mm ss Block comment max length decreased to 22 symbols 18 user supplied number 4 chars space StartTime added to binary file header in Save Blocks 05 12 00 Error No acquisition setup added to Acquisition mode Added
33. isplay and Acquisition modes esses enne nnne rennen innen enne nesn eene 59 0 25 Display modes UR e ee tede eee t e re kohal 59 GEOSSARY d huasi sS hu w aaa u G hu u O au ua 60 PN lai aneemiat 60 lH EHE 60 o M HM A 60 DET 61 je Q 61 E ti aiid haat 61 ret Bile tog REO 61 EI sect DR PEOR IY dea E v lte ERES ERE PERDE TO t 62 OmniLab Manual 7 OmniLab Manual 8 Figures Figure 1 OmniLab splash screen Paese e gum ein uec abe eg a PR eR 20 Figure 2 OmniLab title bar and Run button enne 20 Figure 3 Main mode drop down menu with Calibrate channels mode selected 21 Figure 4 Control part of CalibrateChannels 22 Figures AEGU LOU ED es oa eee M E E s 24 OmniLab Manual 9 About This Manual Use the OmniLab Manual to learn the features functions and operation of OmniLab OmniLab is intended to acquire display and analyze physiological data using a NI DAQ and personal computer To use this manu
34. ld text in this font denotes the messages and responses that the computer automatically prints to the screen This font also emphasizes lines of code that are different from the other examples courier italic Italic text in this font denotes that you must enter the appropriate words or values in the place of these items OmniLab Manual 13 Chapter 1 Introduction to OmniLab This chapter introduces the OmniLab software What Is OmniLab OmniLab is a versatile LabVIEW based or stand alone application designed to meet the data acquisition and data analysis needs of physiological labs by integrating personal computer with physiological monitoring system Using National Instruments data acquisition hardware you can use OmniLab to acquire data from virtually any type of physiological linear voltage signal source While your physiological data is being acquired OmniLab can save it to disk along with your comments After you save your data to disk you can use OmniLab to open your data file for review analysis and export OmniLab Features Data Management Keep track of the user name and the date and time each datafile was acquired Automatically generate entries in a lab journal with time stamped user comments list and other info Data Acquisition Up to 16 analog input channels output triggers for communication with other applications variable sampling rate switch between monitoring and record modes log entire
35. n 4 INSTRUCTIONS Last updated 02 01 02 see also OmniLabHelp Help Help for this VI and online help press Ctrl H and position cursor over the individual item control indicator of interest GENERAL INSTRUCTIONS Press Stop F1 before you change the mode in the main drop down menu under the Run button on the upper left The only exception for this rule is menu item Analysis Setup that can be called during Display mode without stopping When you change something in chart display option and do not see the result press change F5 or F5 In some cases in Display mode you may need to press SHOW BLOCKS F4 or F4 to evoke the change Stop may not react immediately in some situations keep it pressed for a couple of seconds or better use the F1 key When program is running the arrow is black and left LED below is green OmniLab Manual 48 Saving default values For an individual item l 2 2 3 Operate Change to Edit Mode Enter password Right click on item select Data Operations Make Current Value Default File Save For all items on the Front Panel Note use with caution make sure all items on the Front Panel have been set to desired default values l Operate Change to Edit Mode 2 Enter password 2 Operate Make Current Values Default 3 File Save START Double click on OmniLab shortcut on your desktop 1 1 1 Setup Calibration New calibration
36. o before you start your experiment is to calibrate your system OmniLab has built in calibration procedure that allows you to calibrate each channel separately save calibration for future or immediate use update old calibration and change calibration in a datafile The linear 2 point calibration procedure is very simple and consists of defining two points in XY coordinate plane where X is the measured voltage acquired or read value and Y is a real world value measured by some independent calibrated device The calibration equation is thus Y AX B where A is the gain and B is the offset Create New Calibration Start OmniLab select Calibrate channels from main drop down menu and press Run button the arrow Ib OmniLab v 4 0 build File Edit Operate Tools run Ed mmi time ble Calibrate channels f 100 0 Figure 3 Main mode drop down menu with Calibrate channels mode selected OmniLab Manual 21 The CalibrateChannels window view will appear The control part of the view is shown below Select channel to calibrate in the Channel menu Press Acquire for the lst point while supplying the appropriate known signal Type known real world value for the Ist point e g 0 mmHg and press button 1 Press Acquire for the 2nd point while supplying the appropriate known signal Type known real world value for the 2nd point e g 100 mmHg and press button 2 You may notice that the table above is b
37. r OmniLab 3 1 25 06 01 Autoscale Y workaround added 14 06 01 Converted to LabVIEW 6i Bugs in 6 0 discovered got rid of by patching to 6 0 2 and mass recompiling OmniLab 3 10 06 01 Cal file path added to Acquisition Info 20 505 01 OmniLab Manual 38 Online processing revised NaNs bug in save less than 16 channhels to bin ascii fixed 08 05 01 New old format support added to Display mode Stop in DisplayBinLog revised Save Info revised No channels warning added to Acquire mode Check number of blocks revised 01 05 01 Help Link added Online Processing added dp dt heart rate Timer added 25 04 01 Disable stop when recording Print button color changed Save blocks no split revised 22 04 01 Freeze added to Display mode Print Front Panel added to Acquisition mode Print chart revised Full graph mode added to Display mode Grid on off added Acquisition Info placement revised Limit data file to 640 MB added stopping when exceeded Check number of blocks added not recording if exceeded lim 1000 warning about last NEW FORMAT User block comments length increased to 30 symbols 21 04 01 OmniLab Manual 39 Print Front Panel added Display mode revised smart read added time scale and time to read separated 11 04 01 Disable STOP when playing added REWIND added Log START added Acquisition Info revised File In
38. ral Comments 1900 bytes chars 2168 User Header length Pard mete s e MR ere ous 100 bytes On line Parameters 5 4 4 128 bytes array of 4 34 bytes Dale e seed ana p aa ipe sol a q amar buaya 10 bytes SPEELES AA eR ia Su a as RES Pune 10 bytes denderZa4soc ees Meise eel SUVS 6 bytes welghtiaA pex ha RU E E REG IE 4 bytes single float heart weight Z L nem yer erg 4 bytes single float 16 bytes reserved Off line Parameters 10 50 bytes 10x4 10 reserved 2268 User General Header length 2 Block Headers Block Headers Header Current Data End File Length 4 by Block Headers length 4 by Nu mber ot BloGRESu yau EVE es 4 by 2279 Block Comment Max length 4 by WWWW W a CE DS 5 by Ces Ces Ces Ces Ces long integer long integer long integer chars long integer 2284 2288 2168 2267 268 2167 2268 2271 2272 2215 1000 max 2276 44 2280 2283 OmniLab Manual 3l for each block Block Comment start 4 bytes long integer first 2289 Block Comment suls nus 4 bytes long integer BLOCK COMMENCE 25 See ENS S of Block Comments length chars max 44 4 for number one space 30 user one space time 8 chars RR HEY Block Bata starb aema ever 4 bytes long in
39. s needs Visit OmniLab website http igoresha virtualave net LabVIEW OmniLab for more information and updates Igor Kagan kigor tx technion ac il igoresha virtualave net LabVI EW OmniLab
40. s to the same file Note you can append only if you have same number of channels and sampling scan rate as in the file If you use Change file option but select the already existing datafile you will be prompted to replace overwrite the existing file or cancel 2 Monitoring right LED is dark green 2 1 1 Changing number of plots panels for versions before 4 x Channels arrangement chart 1 2 or 4 panels Any channel can be put on any panel plot right click on channel number and select Y scale _for versions 4 x and higher Operate Change to Edit Mode Enter password Right click on chart area Overlay Plots Change plots to desired value A dme oou c CES Run in Acquire or Display mode for an instant then stop OmniLab Manual 53 6 Operate Change to Edit Mode 7 Right click on chart area Stack Plots Note this complicated procedure hopefully will no longer be necessary if NI will fix their bug Channel settings Any channel can be put on any panel plot select appropriate plot next to the channel LED Change color for each channel select appropriate color next to the channel LED Show sel show selected channels show LED is on Show all Hide all 2 1 2 Chart options t scale s time scale default 10 xgrid s time scale division default 0 5 grid on of default on grid color default light grey ysplit arbitrary vertical offse
41. t between channels default 0 disp cal display calibration on off default on all y auto all plots panels autoscale on off below are y autoscale on off individual controls according to number of plots panels stplots F5 change chart options press after entering new settings OmniLab Manual 54 Esc toggles between full screen normal chart 2 1 3 Additional options F6 freeze chart F7 file info Timer on off seconds elapsed from the moment when turned on 2 1 4 Advanced options scans2read controls the smoothness and speed of chart update If the number is small smaller portions of data are added to chart on each iteration more frequently and vice versa When you change it keep track of b log backlog indicator if it is increasing increase scans2read Note that if b log exceeds buffer size set in Acquisition setup see Advanced options the acquisition will be corrupted and current datafile lost 2 2 Recording middle LED is red Press START RECORD F2 to start recording Click in Block comments frame or press F3 to start enter block comments The time block indicator will show recording time in seconds The time rec shows the duration of previously acquired blocks in seconds Press STOP RECORD F2 to stop recording 3 Display mode data retrieval and export Select Display data in the main menu Press Run Select file OmniLab Manual 55
42. ta in Big Endian Form most significant oe byte first Other applications typically expect numeric data to be oe in little endian form least significant byte first In this case OmniLab Manual oo files should be transformed to Little Endian Form before using by these applications In Matlab 5 x there is a parameter in FOPEN oe function MACHINEFORMAT that should be used for these files oo ieee be or b IEEE floating point with big endian byte ordering oe See help fopen for more details on how to read big and little endian files oo lt BEGIN CODE gt oo fid fopen test151100a b 1 1 bin r ieee be filename pathname uigetfile bin log Please choose bin log file 4 4 if filename 0 return end FullName pathname filename fid fopen FullName r ie be pathname READ BINARY HEADER NumberOfChannels fread fid 1 long NumberOfScans fread fid 1 long ScanRate fread fid 1 float32 StartTime char fread fid 8 char Comment Length fread fid 1 long Comments char fread fid CommentLength char 5 READ DATA data fread fid NumberOfChannels NumberOfScans float32 Splot data fclose fid lt END CODE gt OmniLab Manual 47 Appendix F Quick Reference Getting Started Instructions OmniLab versio
43. teger Block Data kengteh ss lbs os S aus 4 bytes long integer WAN WW WES ca wc ri ME e RO UR REUS ER 5 bytes chars Ihere may be empty blocks Maximal number of blocks 1000 Taken by max 1000 21 44 65 65000 bytes 2289 67289 Length of User Header is 67289 3 Binary LabVIEW Header Binary Header Length 4 bytes long integer Group channels settings bytes binary string CKCkCk k k k k k k lt k k k ck k k k k k k k ck k k k k k k ck k k k k k k k k k k k k k k k k k k k ck k k ck ck k k k ck ck k k k k ck k k KKKKKKKKKKKKKK Group channel settings are written by internal LabVIEW procedures according to the following format number of channels long integer 4 bytes for each channel length of channel name long integer 4 bytes channel name 2 3e length of channel name chars single float 4 bytes single float 4 bytes single float 4 bytes tate pU aca ues integer 2 bytes if 2 monopolar then binary data unsigned integers if 1 bipolar then binary data signed integers OmniLab Manual 32 single float 4 bytes short integer 2 bytes short integer 2 bytes s u Gated Sok ed single float 4 bytes Scale xe a mus single float 4 bytes only
44. use stande alone built application OmniLab version LabVIEW 6 0 2 Run Time Engine will be installed as part of OmniLab installation see below Note Users that have previous version of LabVIEW or LabVIEW Run Time Engine should upgrade to 6 0 2 version see below Installing OmniLab To install OmniLab complete the following steps Run OmniSetup Installing from OmniLab CD Insert OmniLab CD to your CD ROM drive If autorun feature is enabled on your machine the setup will start automatically Otherwise double click on OmniSetup exe or select Run from the Windows Start menu and type x OmniSetup in the input box where x is the letter of your CD drive OmniLab Manual 17 Installing from OmniLab floppy diskettes Insert OmniLab diskette 1 to your floppy drive Double click on OmniSetup exe or select Run from the Windows Start menu and type x OmniSetup in the input box where x is the letter of your floppy drive Installing from OmniLab website Download the OmniSetup exe file to temporary directory folder Double click on OmniSetup exe or select Run from the Windows Start menu and type xNOmniSetup in the input box where x is the full path to the directory where the downloaded file is located e g canbe c Windows temp 2 Follow the instructions that appear in the dialog boxes It s highly recommended leaving default settings and options while installing OmniLab Upgrading to LabVIEW 6 0 2 from 6 0
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