VivoSense ® Batch Processing
Contents
1. to the export file Files can be ordered and moved by dragging and dropping the file in order to obtain the desirable file order Renaming a File List A File List can be renamed by right clicking on the corresponding menu item in the File List tree selecting Rename and entering a new file list name Deleting a File List or a File List Folder A File List or any File List Folder can be deleted by right clicking on the corresponding menu item in the File List tree and selecting Delete 2 9 Launching a Batch Process A Batch Process is launched from the main menu in Vivosense by going to Tools gt Launch Batch Process See Figure 3 User Documentation HRV Standard Edition Module Page 9 of 16 VivoSense Batch Processing Module r ES Launch Batch Process Run the specified batch procedure on a list of files Batch Configuration BR Study File List Trial 1 Batch Configuration The batch of commands used to process the list of files Figure 3 Configuring and Launching a Batch Process One of the previously created Batch Procedures as well as a corresponding File List is selected from the Launch Batch Process dialog box The selection of the batch procedure is required input while the File List is optional If no File List is selected the user is prompted with a File Dialog asking to select one or more files This allows the Batch Process to be run without first having to create a File List in the B2. 16
3. 6SSIODS LISTON each ona d P ge adt aces tic perinde dt eC eda 11 4 4 Log nO Mal ii rial la esset en iue etc eoe tee N 12 AS CRI e E 12 5 Additional GomilTialids i bb orbi iii dai 13 5 1 Annotation based Commands ssssssssssssssesss eee rre en res rennen sn nennen 13 5 2 EE eene nnn ennnren Aa IARE EIRA sr entren 14 6 Appendix A Glossary of TermMS ccoccccnonnnccccnnncccnnnnnnnnnnncnnncnnnnnnnnnnnnnnnnnnnnnnnnnnnnnns 16 User Documentation HRV Standard Edition Module Page 3 of 16 VivoSense Batch Processing Module 1 Introduction Vivosense is a visualization and analysis tool designed for compact user interaction and is ideal for processing recording sessions individually VNBatch exe is a non interactive stand alone application designed to apply the same sequence of commands Batch Procedure on an entire list of recording sessions File List in VivoSense The VivoSense Batch Processing Module consists of three components within the Vivosense application the Batch Manager an additional menu item to launch a Batch Process and the actual executable called VNBatch exe This manual describes how to use the Batch Manager for configuring a Batch Procedure and for the creation of File Lists both used as input to a Batch Process It is assumed that the user is familiar with the VivoSense application and it is recommended to read the Vivosense Core manual prior to read
4. N wap wee RM SP SPAR YT 4 CN VIVON ETICS VivoSense User Manual Batch Processing VivoSense Batch Processing Edition 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 Batch Processing 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 2012 Vivonoetics All rights reserved User Documentation HRV Standard Edition Module Page 2 of 16 VivoSense Batch Processing Module Table of Contents Me producto Mi eenn ince tect tadasees cad teas e ae ies ase A A eats usttecs stat tea 4 Its System Requirements eed de nee ee ie ev ne n I dE Toe es ee een ede 4 e A tears ear ata es TORTOR 5 2 1 US 356 5 et Eo TAE ae a tad 5 2 2 Setting up a Batch Process ea bs 5 A A od do An dtes fene 6 3 Managing Batch Proced res c iere er eee tas 7 3 2 Managing File Lists ie cana A ree a a a Tu OA agde Reged 8 3 3 Launching aBateh Process vincia liado 9 4 The VNBatch exe Application oooooccnnnnoccccnnnnnnnnnnnnnnncncnnnnnnnnnnnnnnnnnccnncnnnnnns 11 Ale Patise COntihlle 3 a eub iuto ecd t le ela es 11 4 2 7 SAS A LL ttu E Ct MS 11 4 3 S
5. Procedure The File List can be found in the Batch Manager in the panel below the Batch Procedures User Documentation HRV Standard Edition Module Page 8 of 16 VivoSense Batch Processing Module File List Folders File Lists are organized under the User directory and can be saved in new or existing folders To create a new File List folder right click on the User folder and choose New Folder from the subsequent menu File List folders can be created renamed or deleted by right clicking and selecting New Folder Rename or Delete See Figure 1 Creating a File List A File List is created by right clicking on the corresponding Folder in the File List tree going to New Filelist and selecting the desired file type from the list of imports A Select Files dialog will pop up and prompt the user to select files to be added to the newly created File List The user may select to add files now or add files at any time thereafter See Figure 1 Adding Files to an Existing File List Additional files can be added to a File List by right clicking on the File List selecting Add Files and adding the new files using the resulting dialog During a Batch Process the sessions within a File List are processed in the order they are shown in the Batch Manager It may be desirable to arrange these files in a specific order particularly if an export Batch Command is used as exported data will be appended in this specific order
6. This interaction is implemented by writing any output to a log file see section 4 4 Deleting Command from a Batch Procedure A Batch Command can be deleted by right clicking on the command in the Batch Procedure tree and selecting Remove to remove it from the tree Renaming a Batch Procedure A Batch Procedure can be renamed by right clicking on the corresponding menu item in the Batch Procedure tree and selecting Rename and entering a desired name Changing Settings of Batch Procedure Command A Batch Command that has been configured and added to a Batch Procedure can be edited at any time To edit the Batch Procedure view the Property Window by pressing F4 or the Property Window icon on the toolbar see the VivoSense Core Manual By selecting the Batch Command in the Batch Manager we will be able to edit that Batch Command s properties Rearranging the Order of Batch Command The Batch Commands are executed in the order they appear within a Batch Procedure A Batch Command can be moved up or down within the Batch Procedure by right clicking on the Batch Command menu item in the Batch Procedure tree and selecting Move Up or Move Down 3 2 Managing File Lists A File List is a collection of sessions used by a Batch Process It is a convenient way of organizing sessions for multiple uses All the files within one File List must be of the same type in order to guarantee that they can be processed by the same Batch
7. atch Manager Only vsn files can be batch processed in this way Note that while a Batch Process is configured and launched from within Vivosense it is runs as a stand alone application that will continue to execute even after Vivosense is shut down User Documentation HRV Standard Edition Module Page 10 of 16 VivoSense Batch Processing Module 4 The VNBatch exe Application r Batch Process Sessions Log information Filename Status Date Command Text Subject 1 vsn OK 4 29 2011 Open File Subject 2 vsn OK 4 29 2011 QDC Autom Command not found Subject 3 vsn OK 4 29 2011 Export Data O Subject 4 vsn OK 4 29 2011 Export Data x Subject 5 vsn ZEW amp 4 29 2011 Reset FVC Command not found Y Subject 6 vsn OK Subject 7 vsn Processir Subject 8 vsn Waiting Subject 9 vsn Waiting Subject 10 vsn Waiting 4 m p 4 n p Pause Status mmm Processing Subject 7 vsn Writing data to Subject 7 20110317083644 002707 data csv Figure 4 VNBatch exe during execution VNBatch exe is intended to be executed without user interaction It opens all the session specified in the File List in order and performs all the Batch Commands specified in the Batch Procedure Figure 4 shows a screenshot of VNBatch exe during execution while Figure 5 shows the same process after the execution is completed 4 1 Pause Continue The Pause Continue button a
8. er by opening a vsn file or by importing raw data from any of the supported sensor formats Opening a vsn file The Batch Procedure is started by right clicking on User gt New Vivosense Batch Procedure Importing a support sensor format The Batch Procedure is started by right clicking on User gt New Import Batch Procedure gt Import file where Import file is a generic placeholder for the specific import type used with this Batch Procedure Depending on the type of import the user may be prompted to specify additional information related to the import in the same way as he would by importing a file of this type via File gt Import Hardware File gt Import file This additional information will be stored together with any other Batch Procedure configurations for the later use in a Batch Process The default name for the procedure is New Config n where n 1 2 3 and can be changed by the user A Batch Procedure can be deleted by right clicking on the corresponding menu item in the Batch Procedure tree and selecting Delete Adding Commands to a Batch Procedure A command can be added to a Batch Procedure by right clicking on the corresponding menu item in the Batch Procedure tree and selecting Add Command There are some universal commands that apply to all sessions such as all the Export commands Template commands or the Set Start Time command However most commands are specific to the particular ses
9. h mode Make all annotations visible A menu item called Show all Annotations will be added to the Session gt Annotations menu When this item is selected all annotations will be made visible Make all annotations invisible A menu item called Hide all Annotations will be added to the Session gt Annotations menu When this item is selected all annotations will be made invisible Make selected annotations visible A menu item called Show Annotations will be added to the Session gt Annotations menu When this item is selected a dialog opens as shown in Figure 6 E ES Show Annotations Show all annotations with the specified name Name Search String Description Search String Case Sensitive True Name Search String The string to search for within the annotation name Figure 6 Select annotations by name and description User Documentation HRV Standard Edition Module Page 14 of 16 VivoSense Batch Processing Module After clicking ok the application will select all annotations that match don t match the search strings if the option match search string is selected de selected and make them visible In addition there is the option to set the matching to case sensitive Make selected annotations invisible Same as last command except that the selected annotation will be made invisible User Documentation HRV Standard Edition Module Page 15 of 16 Viv
10. ible annotations yield multiple exports to the same file separated by a blank line Overlapping annotations will result in the same data being exported multiple times Export Statistics by Annotation menu item The command Session gt Annotations gt Export Statistics by Annotations will export all the statistics within the time range of any visible annotation Multiple visible annotations yield multiple exports to the same file separated by a blank line Statistics will be calculated over the entire annotation regardless of any potential overlap Duplicate Annotations menu item The command Session gt Annotations gt Duplicate Annotations will create duplicates of all currently visible annotations A dialog will pop up that lets the user enter a shift in seconds of the start and end time of the annotation In addition the user can enter annotation name and description It is recommended to choose unique names so that the resulting annotations can be removed easily If the resulting start time of the duplicate annotation is earlier than the session start time then the start time shall be set to the session start time If the resulting end time of the duplicate annotation is later than the session end time then the annotation end time shall be set to the session end time If the resulting end time of the duplicate annotation is earlier than the annotation start time then the annotation end time shall be set to the ann
11. ing this manual on Batch Processing A Batch process allows the user to apply the same set of commands to a set of files to save time eliminate human errors or to easily reproduce previous results 1 1 System Requirements This module is an add on processing module and requires the VivoSense core software User Documentation HRV Standard Edition Module Page 4 of 16 VivoSense Batch Processing Module 2 Batch Process A Batch Process is executed as a stand alone application called VNBatch exe It is set up and configured from within Vivosense via the Batch Manager Note VNBatch exe is a separate application that will continue to execute even if Vivosense is terminated 2 1 Use Case The Batch Process is intended to standardize the processing of multiple sessions Depending on the details of the Batch Procedure it is expected that all the sessions have certain commonalities with respect to duration available channels and the type of hardware use to collect the data in order to get consistent results across all sessions 2 2 Setting up a Batch Process Setting up a Batch Process follows three steps 1 Create a Batch Procedure using Batch Manager 2 Compile a File List using Batch Manager 3 Launch VNBatch exe via Tools gt Launch Batch Process User Documentation HRV Standard Edition Module Page 5 of 16 VivoSense Batch Processing Module 3 Batch Manager The Batch Manager is a graphical component
12. llows the user to temporarily interrupt the execution of the Batch Process This is useful if one wants to minimize the CPU usage of VNBatch exe in order to perform other tasks This option is grayed out after completion of the process Figure 5 4 2 Status Bar There are up to two progress bars in the status bar of the application The first one indicates the overall progress of the Batch Process the second one indicates the progress of the session in process When the Batch Process is finished executing the status bar will read Batch process completed see Figure 5 4 3 Sessions Listbox The list box under Sessions shows all the file names of all the sessions in the File List The status is indicated in the Status column and reflected by an icon User Documentation HRV Standard Edition Module Page 11 of 16 VivoSense Batch Processing Module 4 4 Log Information The Log information list box on the right side of VNBatch exe displays details regarding the processing of a particular session It can be viewed by selecting the corresponding file name in the Sessions list box In general there is one entry for every Batch Command with the icon indication failure red x or success green check mark Additional information may be available for some commands info icon E Batch Process l c Sessions Log information Filename Status Date Command Tex Subject 1 vsn OK 4 29 2011 Open File O Subject 2 vs
13. n oK o 4 29 2011 QDC Calibration was successful RC gain 133 284 AB ga Subject 3 vsn OK 4 29 2011 set parameter V Kratio 1 085648 Subject 4 vsn OK 4 29 2011 QDC Automatic ES Subject 5 vsn Failed 4 29 2011 Export Data ORT O 4 29 2011 Export Data Subject 7 vsn OK 4 29 2011 set parameter V Gain 1 Subject 8 vsn OK 4 29 2011 set parameter M IsCalibrated False Subject 9 vsn OK 4 29 2011 Reset FVC Subject 10 vsn OK Batch process completed Figure 5 VNBatch exe after execution is completed 4 5 Log File Every Batch process writes out a log file called DOC Vivonoetics VivoSense Logs Logfile Time Date txt Where DOC is the user Document folder Time is the creation time in the format hh mm ss and Date is the file creation date in the format mm dd yyyy User Documentation HRV Standard Edition Module Page 12 of 16 VivoSense Batch Processing Module 5 Additional Commands It is often desirable to perform a command only on a subset of a session In this case it is useful to identify the region by an annotation In addition there a commands for the management of annotations that can be used from batch mode 5 1 Annotation based Commands Export Data by Annotation menu item The command Session gt Annotations gt Export Data by Annotations will export all the data within the time range of any visible annotation Multiple vis
14. oSense Batch Processing Module 6 Appendix A Glossary of Terms The following is a list of frequently used Batch Process terminology Batch Command A Batch Command is any procedure performed on an open Vivosense session Currently any interactive Vivosense command launched from within the Session menu in Vivosense is a valid Batch Command Note the list of commands available is session depended For instance the command Automatic Artifact Marking is only available for sessions containing an ECG waveform Batch Procedure A Batch Procedure is a sequence of Batch Commands Batch Procedures are created configured and stored using the Batch Manager Batch Process A Batch Process is the execution of a windows application that performs a selected Batch Procedure on a list of selected files The files used can either be vsn files or any files of the supported import types Note only files of the same type can be processed within the same Batch Process Batch Manager The Batch Manager is the graphical component in Vivosense used to manage Batch Procedures and File Lists File List A File List is a either a collection of vsn files or a collection of files of any of the supported import files Note all the files within a File List must be of the same type VNBatch exe VNBatch exe is the stand alone Windows application that executes the Batch Processes User Documentation HRV Standard Edition Module Page 16 of
15. of Vivosense used to set up and manage Batch Procedures and File Lists It is launched by selecting View gt Batch Manager pressing the F8 keyboard button or clicking the Batch Manager icon E The Batch Manager consists of two components the top component is a collection of all the Batch Procedures organized in a tree view within the root directory User On opening the Batch Manager the User root folders will be empty Figure 1 shows an example of the Batch Manager after it has been populated with relevant Batch Procedures and File Lists Batch Manager I e User AY QDC Automatic BY Automatic Artifact Marking Figure 1 Batch Manager User Documentation HRV Standard Edition Module Page 6 of 16 VivoSense Batch Processing Module 3 1 Managing Batch Procedures A Batch Procedure is a set of commands that is to be performed on a single file in a defined order Since the Batch Process does not accept user input other than to Cancel the batch procedure therefore all command properties must be predefined The time location or time range cannot be selected for a batch procedure Therefore all commands listed under the Session menu are available as options for a batch procedure however the commands listed in the sub menus on the Synchronized Chart Panel SCP will not be available Creating a Batch Procedure Every Batch procedure is initiated by loading a recording session eith
16. otation start time E Merge Annotations menu item The command Session gt Annotations gt Merge Annotations creates a new annotation for every consecutive pair of visible annotations The earlier later of the two annotations will define the start end time of the new annotation When this item is selected a dialog will pop up and let the user enter an annotation name and description for the newly created annotations It is recommended the user chose unique names such that the resulting annotations can be removed easily E Clone Annotations as HRV Regions menu item The command Session gt Annotations gt Clone Annotations as HRV Regions creates a new HRV Region annotations that match the start and end times of the currently visible annotations The resulting HRV region must not overlap with an already existing HRV region By default all annotations created by command are visible User Documentation HRV Standard Edition Module Page 13 of 16 VivoSense Batch Processing Module Remove Annotations menu item The command Session gt Annotations gt Remove Annotations will PERMANENTLY remove all the visible AND removable annotations 5 2 Annotation Management This is a set of commands for managing annotation properties such as adding deleting and showing hiding annotations based on the text and description The purpose is to streamline the annotation management and to make the capability available in batc
17. sion import type and depend on the user license Therefore the Batch Manager requires that there be an open session preferably of the same type as the ones the Batch Procedure is intended for or the user will be prompted to open a session Figure 2 VivoSense e You need an active session in order to add a command Figure 2 Adding a command without an active session User Documentation HRV Standard Edition Module Page 7 of 16 VivoSense Batch Processing Module Since a Batch Process is non interactive the batch commands must be pre configured There are three types of user interactions that can be performed after launching a command Set user defined parameters prior to performing a calculation This interaction is implemented by setting up a Batch Command in the same way in which a command is executed on a session in the interactive mode not in batch mode Note there are small differences between executing a command in interactive and batch mode e g launching an export file with the default application after a command is completed is convenient in interactive mode but launching an export file for every session being processed by a Batch Process will slow the process and may be undesirable Make a decision based on the outcome of a calculation This interaction is implemented by automatically selecting the default option rather than asking for user input Display the result of the calculation to the user
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