VivoSense ® Synchronization and Merge
Contents
1. cccccccsssseccccceeeseceeecaeseeceesseeeseceeseaeaseeeesseeaeeeessseaaecesesseaaeceeesseseceesssanseeees 13 43 Merging ANNOIATO Srs A ea 14 4 4 Resolving Ghanmel C OmilictS sida vio 14 UserDocumentation HRV Standard Edition Module Page 3 of 14 VivoSense Synchronization Module 1 Introduction 1 1 Synchronization and Merge Module for VivoSense This manual describes the Synchronization and Merge Module for VivoSense A brief background on the problem of synchronization as it relates to physiological data collection will be discussed and then the specific features and solutions found in VivoSense will be outlined To use the Synchronization and Merge Module users must already possess a fully registered copy of the core VivoSense application This is a prerequisite for all supplementary modules and provides the framework through which interactions with data occur Likewise users should be familiar with the import modules for all desired data types before using this module As will be explained later the import and synchronization processes are tightly integrated and knowledge of one will help in understanding the other User Documentation HRV Standard Edition Module Page 4 of 14 VivoSense Synchronization Module 2 Synchronization Background 2 1 The Integration Problem VivoSense is a hardware agnostic physiological data visualization and analysis platform In addition to supporting a wide variety of hardw2. process he or she may simply press the Escape key or click on the button of the current synchronization process For example if Point Synchronization is currently being used and the user decides to cancel he or she can just press the Escape key or press the Point Synchronization button again to cancel the operation Likewise any closing or opening of new sessions will also cancel the current synchronization process Synchronization Preferences Synchronization preferences can be found by clicking on the Tools menu item then selecting Preferences and opening the Synchronization and Merge tab The following options are currently available 1 Intelligent Sync Accuracy Can be set to Low Normal High or Highest and controls the resolution of the Intelligent Synchronization algorithm s search for the optimal synchronization point Typically this option should be left at its default Normal but if the results are not satisfactory the High or Highest setting may work better Note Choosing High or Higher will significantly increase the time needed to perform Intelligent Synchronization especially on large high resolution files Reviewing Synchronization Session Axis Lock To facilitate the review of the synchronization process the Synchronization Module offers a Session Axis g A Lock button which will link all open sessions together so that they show the same timeline Scrolling on one will cause scrolling on the other which all
3. B 8 B 5s je Time Diff 00 00 20 942 Cursor Diff 295 8904 Search complete Figure 5 Intelligent Synchronization Annotations indicating the optimal synchronization point persist for all secondary channels These can be reviewed later and removed by the user if desired To achieve the highest level of accuracy for intelligent synchronization it is important to note the following concepts User Documentation The channels chosen for synchronization must exhibit similar shapes or patterns The magnitude of the data need not match but in order to find synchronization points the characteristics of the data must be similar For example it is possible to match accelerometer data across multiple devices if they are being worn by the same person Even if they were worn by different subjects if a concurrent event can be found in both recordings for instance a tap it should be possible to synchronize off of that region Although not absolutely necessary synchronization works best when comparing data with similar sampling rates If one channel is sampled at a significantly faster rate try using a trend channel to bring it in line with the other channels and then use the trend for synchronization Page 10 of 14 HRV Standard Edition Module VivoSense Synchronization Module Cancelling Synchronization If after pressing one of the synchronization buttons the user wishes to not continue with the synchronization
4. in each of the files in question will populate the leftmost column Just like the normal mport Configuration Dialog the task at this point is to map channels from the leftmost column to channels that can be handled by VivoSense Figure 7 Es Merge Configuration Wizard File Configuration Start Time 07 51 23 03 11 2010 Merge Channel File Name Channel Type VivoS5ense Channel Sample Rate Hz SEM_ecg2 2 3 21 10 SEM vsn Ignore Select Type SEM_ecg1 2 3 21 10 SEM vsn Select Type SEM belt 2 321 10 SEM vsn Ignore Select Type Temperature SEM accL 2 3 21 10 SEM vsn Select Type EEG SEM T skin 2 321 10 SEM vsn EMG Select Type SEM accV 1 21 10 GEM y Respiration Sal SEM accV 2 3 21 10 SEM vsn Parum Select Type SEM accW 2 321 10 5EM vsn GSR Select Type Figure 7 Merge Configuration Dialog VivoSense users will notice that two columns in the Merge Configuration Dialog have changed The second column is now the File Name column and it indicates the file to which each channel in the leftmost column belongs Additionally the rightmost column is now the Sample Rate column and it provides a non editable view of the sampling rate for each channel 4 2 Merging Channels Typically when users merge channels from two or more sessions they want them to remain distinct and untouched in the new file For example perhaps one has a file containing an ECG waveform and three accelerometer channels whereas another file re
5. VIVONOQETICS Vivosense User Manual Synchronization and Merge Module VivoSense Synchronization Module Version 2 0 Vivonoetics San Diego Office 3231 Huerfano Court San Diego CA 92117 3630 Tel 858 876 8486 Fax 248 692 0980 Email info vivonoetics com Web www vivonoetics com VivoSense Synchronization Module Cautions and disclaimer VivoSense software is not a medical diagnostic tool It is for research and investigational purposes only and is not intended to be or to replace medical advice or review by a physician Copyright Notice Copyright O 2011 Vivonoetics All rights reserved User Documentation HRV Standard Edition Module Page 2 of 14 VivoSense Synchronization Module Table of Contents la A o ee ee 4 1 1 Synchronization and Merge Module for VivoSense oocccccccnncnccconcnccconnnncononnnnononnnnononnnnnonancnnononens 4 2 OVMECMFONIZATION BAC UA tee E ee ee Ec tas UE DM Ld 5 Zales PhedntegralohProblelhtsauud cessa iioc ete vradelcu o pi 5 22 COyhchroHzauon t VIVOSODISQ scatet A 5 2 3 The Synchronization and Merge User Interface oooocccccccccnnconccononcconcnononncnnononanncnnnnonancnnnononanenos 5 Se IMEI DS o a 7 dle AMPOrINna Dalai cal 7 32 SVMGHKONIZING Dalai EE 7 A INMGTOING Dala FOSA 13 4 1 Merge Configuration Dialog cccccoconconccccconnnnncnononcnnnnonnnncnnnnonnnncnnnnnnnnncnnnnonannnnnnnnnnnnnnncnnnanenss 13 4 2 Merging Channels
6. are formats VivoSense also facilitates the analysis of any other data through its generic Excel and European Data Format EDF imports Moreover new hardware platforms are being added to the system all the time and so VivoSense is quickly becoming the single integration point for any sensor data a user might have With streamlined access to data from a wide variety of different sensor systems the primary complication after acquisition centers around how to integrate the various recorded data It is clearly advantageous to be able to view and interact with all data streams in one synchronized interface rather than having to use separate windows or even applications to perform one s analysis However this goal is deceptively difficulty to achieve Numerous obstacles such as different file formats non synchronized start times and dropped packets in wireless recordings all make the process of aligning data from different hardware very challenging 2 2 Synchronization in VivoSense The Synchronization and Merge Module in VivoSense aims to address the above problem through the use of a streamlined synchronization and merge process that allows users to tie disparate data streams together using easily understood visual markers and annotations VivoSense will further speed up the potentially tedious synchronization step with its automated synchronization algorithms which can instantly determine with millisecond accuracy the ideal synchronization po
7. corded at the same time includes two respiration channels These six channels represent records of distinct physiological processes and consequently can be easily merged without conflict into a new file However there are also times when the same sensor data may be shared across multiple files An ECG recording may have been done a multiple times during a study with gaps of a few minutes or hours in between each recording For these situations the VivoSense merge functionality provides the concept of channel merging Channel Merging combines the data from multiple channels across multiple files into the same channel in the newly merged file Multiple respiration ECG or accelerometer data streams can be combined together to create a single time synchronized channel To achieve this simply choose the same VivoSense Channel User Documentation HRV Standard Edition Module Page 13 of 14 VivoSense Synchronization Module name for multiple input channels in the Merge Configuration Dialog After clicking Done to begin the merge VivoSense will alert the user that channel merging will occur Figure 8 Confirm Channel Merge Multiple channels have been assigned to the same VivoSense channel and will be combined into a single channel If overlap occurs the first channel s data will be used Would you like to continue Figure 8 Channel Merging Note In cases where data from channels overlaps the data from the channel with the
8. earliest start time will be used Also of note is that for evenly sampled data streams channel merging may introduce a timing error of up to 1 sampling rate seconds as the merged channels may not be perfectly synchronized 4 3 Merging Annotations In addition to the data in the selected channels annotations will also be merged If both files contain the same annotation only one copy will be kept 4 4 Resolving Channel Conflicts When performing a merge with files that do not contain any of the same sensor types this process is very straightforward However if the channels exist in two different files then one needs to make a decision about how best to configure the merge If the candidate files together contain more than the allowed number of channels for a particular sensor type then the user must select a subset of the available channels for inclusion The channels selected can be from the same file or both the only constraint is the number selected Although the number of channels supported for each data type is limited VivoSense does allow the specification of up to eight Generic channels which can be used for any type of data Users can visualize and trend these generic channels but they will not receive the same kind of processing that they otherwise would if they were specified as say an ECG or Respiration channel User Documentation HRV Standard Edition Module Page 14 of 14
9. elected simply click no at the prompt and then choose new synchronization points The synchronization annotations will be updated as changes are made To only synchronize a subset of the open sessions select points on the desired sessions and then click the Point Synchronization button again A confirmation will be displayed and synchronization can then be performed on just the selected sessions After synchronization is complete the start times of the secondary sessions will be updated to reflect the points chosen and the temporary annotations will be removed To view the quality of the synchronization try using the Session Axis Lock feature see Session Axis Lock section User Documentation HRV Standard Edition Module Page 8 of 14 VivoSense Synchronization Module Annotation Synchronization If the two sessions marked for synchronization both contain an annotation that delimits a similar point in time then annotations can be used for alignment A common example of this would be an event marker that was inserted at the same time for two different hardware systems during a recording To begin using this synchronization method press the Annotation Synchronization button o on the toolbar A tooltip with instruction will appear at which point you may select one annotation from a chart on each of the sessions Annotations may be selected by either left clicking on them or by dragging a region over an annotation If region selected co
10. he Point Synchronization process Annotation Synchronization Clicking this button will begin the Annotation Synchronization process Intelligent Synchronization Clicking this button will begin the Intelligent Synchronization process User Documentation HRV Standard Edition Module Page 6 of 14 VivoSense Synchronization Module 3 Synchronizing Data Files 3 1 Importing Data The first step in any VivoSense analysis is to import one s data The synchronization process is no exception as all data to be synchronized must first be loaded into the software This step can be performed by going to the File Menu and selecting Import Hardware File followed by the type of file to import If the desired data files have already been imported and saved in the VivoSense file format use the File gt Open vsn File option to load in the data For more details on the import process see the VivoSense Core Manual 3 2 Synchronizing Data The synchronization step is vital in ensuring that data recorded on different sensor hardware are aligned properly for analysis To begin the synchronization process make sure the relevant files have been loaded into VivoSense and that their respective sessions tabs are visible Next press the Synchronization Layout button on the toolbar 5 Your Synchronized Chart Panel SCP will update to show all open sessions vertically tiled in your main window Figure 2 This layout is used to make the sync
11. hronization process easier and faster Once finished with synchronization click the Synchronization Layout button again to switch back to the default tabbed session view ES VivoSense o Ele Session Vie ndow Help View Tools Wi H Sb oa Bors DP RGE SyncTest 2b vsn Layout Start Time 20 34 10 089 Duration 00 00 04 846 Session Start Time 20 33 03 Duration 00 27 07 A BioRadio Ecgl Time 20 34 11 662 Cursor 6 660959 SyncTest 2a vsn Layout Start Time 15 41 38 083 Duration 00 00 05 187 Session Start Time 15 40 09 Duration 00 27 07 ii ieii A BioRadio Ecg1 15 41 42 000 Time 15 41 43 250 Cursor 1 90411 Value Ecg1 0 0808296 Figure 2 The Synchronization Layout One other important concept in aligning two files is the idea of primary and secondary sessions In this case the primary session is the file to which the other sessions will be aligned In other words the primary session s start time remains fixed whereas the secondary session s timeline is modified to match the primary s When performing synchronization operations the primary session is indicated by the order in which User Documentation HRV Standard Edition Module Page 7 of 14 VivoSense Synchronization Module sessions are clicked For instance with Point Synchronization when asked to choose parallel points on two different sessions the session first clicked by the user wi
12. int The process of combining two sensor data files into one integrated file is broken up into two distinct steps in VivoSense First users can use state of the art visualization techniques and algorithms to align the timestamps of the files in question Then in a straightforward and clean interface users can choose which channels to merge together into the final file This allows a very fine level of control over the process and gives the user a quick means to eliminate unnecessary channels from the merged file These two processes will be discussed in detail below along with screen shots that illustrate the entire synchronization and merging procedure 2 3 The Synchronization and Merge User Interface Once the Synchronization and Merge Module has been purchased a new group of icons will be accessible on the VivoSense toolbar Figure 1 File View Tools Window Help Sd AA sh PEE Figure 1 Synchronization and Merge Icons The functionality of each of the new icons is explained below User Documentation HRV Standard Edition Module Page 5 of 14 VivoSense Synchronization Module Is Merge Clicking this button will begin the merge process for all open files Session Axis Lock Clicking this button will lock X axis scrolling for all open sessions Synchronization Layout Clicking this button will toggle between tabbed and vertically tiled sessions Point Synchronization Clicking this button will begin t
13. ll be the primary session and the others the secondary sessions Users may use a variety of methods to synchronize the data between the sessions shown Each of these techniques is accessible from the toolbar menu and is explained in detail below Point Synchronization If the location of two parallel points in time can be located on a channel in each of the sessions then the secondary session s time can be updated to match the primary session s timeline To perform this type of synchronization first zoom in on each session until a known parallel time is visible on each chart Then select the Point Synchronization button from the toolbar A tooltip will appear indicating that you should select a point on the primary session Do so by left clicking at the desired location on any chart in the primary session A temporary annotation will be created at the point selected Figure 3 Next select a corresponding location on one or more secondary session channels A temporary annotation will be created for each point selected and once a selection has been made for each session the user will be automatically prompted to perform synchronization Eile Session View Jools Window al bd gt A gt A SyncTest 2b vsn Layout Start Time 20 34 10 089 Session Start Time 20 33 03 Duration 00 27 07 4 BicRadro Chart Figure 3 Point Synchronization If edits need to be made to the locations s
14. ntains more than one annotation the first one will be chosen for synchronization Figure 4 File Session View Tools Window Help haria do sD PAG SyncTest 2b vs vsn Layout Start Time 20 34 45 367 Duration 00 13 33 739 v Session Start Time 20 33 03 Duration 00 27 07 400 400 AccX nue AM 3 y a x par 200 AIA onn Time 20 41 24 339 Cursor 784 2466 Value AccX 231 0428 SyncTest 2a vsn X Session Start Time 15 40 09 Duration 00 27 07 300 Layout Start Time 15 46 56 521 Duration 00 03 23 434 Time 15 48 24 857 Cursor 163 9175 Value AccX 234 7647 Filtering AccX Figure 4 Annotation Synchronization After a selection has been made for each open sessions or for a subset as discussed in the Point Synchronization section a prompt will be displayed and synchronization can be performed Note Sessions will be synchronized to the beginning of the annotated regions Intelligent Synchronization Oftentimes it is possible to precisely align two data streams in time by analyzing the data itself to determine the point at which the signals best match up This process can be much faster and significantly more accurate than manual synchronization for suitable data streams To use this method of synchronization press the Intelligent Synchronization button KO on the toolbar A tooltip message with instructions will appear at which point you may select a regi
15. on or an entire chart from each of the open sessions An annotation may also be selected to demarcate the desired region for synchronization User Documentation HRV Standard Edition Module Page 9 of 14 VivoSense Synchronization Module Note If multiple channels are present on a particular chart then data from the first channel on that chart will be used for all calculations Once selections have been made VivoSense will process the data to find the optimal synchronization point After each point has been found a prompt will be presented to the user showing them the proposed new start time for this session along with an estimate of the quality of the synchronization The user may then choose to use this point reject it or cancel the process altogether Figure 5 BB VivoSense ole z File Session View Tools Window Help GS 4a oy SO BEBS 66 SyncTest Sb vsn x Layout Start Time 01 40 38 000 Duration Entire Session Session Start Time 01 40 38 Duration 00 02 25 L BeeX Y The best new start time 99 4 accuracy for SyncTest Sa vsn was determined to be01 01 00 01 40 53 131 a shift of 4078 15 12 34 5863872 Would you like to accept thi z 0 0 LAY MecX 100 100 200 200 300 300 E 400 500 500 600 700 700 4 800 1 1 i r 16 53 27 717 165340 000 16 54 00 000 16 54 20 000 16 54 40 000 16 55 00 000 16 55 20 000 16 55 28 590 wX B5 d B
16. ows users to compare how well channels from each session have been synchronized Figure 6 Session Start Time 07 51 23 Duration 25d12 26 10 ia ReadiBand i f Trend Zero Crossi LP M NI ul Y Y 200 100 de ni Po Y 1148 30 344 000 Time 23 05 15 446 Cursor 364 726 EPA VEN Layout Start Time 19 57 41 812 Duration 15 50 48 532 Session Start Time 23 55 23 Duration 07 55 24 Figure 6 Session Axis Lock User Documentation HRV Standard Edition Module Page 11 of 14 VivoSense Synchronization Module Once satisfied with the results simply click the Session Axis Lock buttons again to return to normal scrolling Now that your sessions have been synchronized please refer to the Merging Data Files section to learn how to merge files together User Documentation HRV Standard Edition Module Page 12 of 14 VivoSense Synchronization Module 4 Merging Data Files After files have been synchronized their data channels can be merged into a single unified file This is done from the File gt Merge Open Files menu option which allows selection of multiple files for merging The merging process is described in detail below 4 1 Merge Configuration Dialog The Merge Configuration Dialog looks and operates similarly to the mport Configuration Dialog see Core Manual but serves a slightly different purpose When the dialog opens a list of all channels available
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