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Name

wave - waveform analyzer, viewer, and editor

Synopsis

wave -r record[+record ...] [ options ... ]

Description

wave can be used to view the specified WFDB record or records on any display controlled by an X11 server. It includes facilities for interactive annotation editing. The keyboard and mouse are used to control the display interactively. First-time users should read the WAVE User’s Guide, available at http://physionet.org/physiotools/wug/ (or, while wave is running, choose User’s Guide from the Help panel).

If you specify more than one record, a separate wave process is started for each record. Note that all records to be opened must be listed in a single command-line argument following -r, with + characters (not spaces) between the record names. See ‘Running two or more WAVE processes’ below.

Use the left mouse button to make selections, and the right mouse button to open menus (indicated by triangular glyphs at the right end of some buttons). See the Guide or choose Annotation Editing from the Help panel).

Options are:

-a annotator
Open the specified annotation file for the previously specified record or records.
-dpi xx[xyy]
Calibrate wave for use with a display having a resolution of xx (by yy) dots per inch.
-f time
Open the record(s) beginning at the specified time.
-g
Use shades of grey only, even on a color monitor.
-H
Read the signal files in high-resolution mode (default: standard mode). These modes are identical for ordinary records. For multifrequency records, the standard decimation of oversampled signals to the frame rate is suppressed in high-resolution mode (rather, all other signals are resampled at the highest sampling frequency).
-m
Use monochrome (usually black and white) only, even on a color or greyscale monitor. The line styles selected by the -m option may be easier to distinguish on some greyscale monitors than the default shades of grey.
-O
Use overlay graphics for maximum speed and display quality if possible. This is the usual default if the X server supports a PseudoColor or GrayScale visual. This option exists only to force use of overlay graphics if a different mode has been chosen as the default.
-s signal-list
Initialize the signal list. By default, the signal list includes all available signals, in numerical order.
-S
Use the standard (shared) color palette, even if it is possible to modify the palette. Using this option conserves color resources if you have other applications that use non-standard colors, at the expense of some speed in redrawing the display. The -S option may be used in combination with the -g option if desired.
-Vx
Set display option x. See ‘Display Options’ below for details.

Note that wave queries the X server to determine the display capabilities and resolution; it is not necessary to use the -g, -m, or -S options unless you wish to restrict wave’s use of the available capabilities. Use the -dpi option to override the server’s default resolution if it is incorrect and cannot be changed otherwise (see comments below under ‘Resources’).

The system on which wave runs (the ‘‘host’’ system) need not be the same as the system to which your keyboard, mouse and display are connected (the ‘‘local’’ system), provided only that the host and local systems are on the same network. If you wish to run wave remotely, simply log in to the host using ssh, which normally handles display redirection automatically. If you use some other method to log in remotely, such as rlogin (not recommended) or telnet (not recommended), it is usually necessary to grant permission for the host system to open windows on the local system’s display (generally, this is accomplished using xhost on the local system; see the documentation for your X server for details), and to set the DISPLAY environment variable on the host system appropriately (if the local system runs UNIX, the value of DISPLAY should be local-hostname:0.0 in most cases; again, consult your X server documentation).

Environment

wave uses many environment variables; they are listed in this section roughly in order of importance. Many of them need not be set at all, since wave uses reasonable default values in most cases. Those that are set must be set on the host system.
DISPLAY
The name of the X server and display you are using (see above). If you are using wave locally, or if you are logged in via ssh, DISPLAY should be set automatically and should not need to be changed.
WFDB
The database path (see setwfdb(1) ). If not set, wave can find database files only in the builtin WFDB path. If you edit annotation files and wish to reopen them later, be sure that the current directory (in which wave writes any edited annotation files) is the first directory in your database path.
WFDBCAL
The WFDB calibration file (see setwfdb(1) and wfdbcal(5) ). If not set, wave reads the builtin default calibration file; if this is not accessible, wave may not scale signals other than ECGs correctly.
WAVEMENU
The name of the analysis menu file (see below); if not set, wave uses wavemenu if it exists in the current directory, or $MENUDIR/wavemenu.def otherwise.
SHELL
The command interpreter used within the Analysis Commands window; if not set, wave uses /bin/sh (the Bourne shell). Other shell-related variables, such as PATH, are also significant when wave is running commands within the Analysis Commands window.
EDITOR
The name of the text editor to be used for modifying the analysis menu file and the log file. If not set, wave uses textedit (a simple editor included with the XView toolkit).
PRINTER
The name of a printer to be used for paper output; if not set, wave uses the default printer.
PSPRINT
The command used to print PostScript data from the standard input; if not set, wave uses ‘lpr -P$PRINTER’.
TEXTPRINT
The command used to print text from the standard input; if not set, wave uses ‘lpr -P$PRINTER’.
ANNTAB
The name of a file that contains custom annotation definitions (see ‘Resources’, below, for details). If not set, wave uses standard annotation definitions only.

The environment variables below are not needed unless the wave binary distribution, or XView, has been installed in non-standard directories:

HELPPATH
The path for XView spot help; if not set, wave initializes it to /usr/lib/help. wave’s own spot help is in $HELPDIR/wave, which is appended to the end of HELPPATH by wave.
HELPDIR
The directory in which wave’s help directory is located; if not set, wave uses /usr/local/help.
MENUDIR
The name of the directory that contains the default analysis menu file; if not set, wave uses /usr/local/lib.
RESDIR
The name of the directory in which system-wide default X11 resource files are kept; if not set, wave uses /usr/lib/X11/app-defaults. XUSERFILESEARCHPATH, XAPPLRESDIR, and XENVIRONMENT are also used, together with HOME and USER, to locate resource files (see X(1) ).

Resources

You can control many aspects of wave’s appearance and behavior by setting its resources. If you are not familiar with this concept, refer to an introductory book on using the X Window System, such as Darwin, Quercia, and O’Reilly’s X User’s Guide: Open Look Edition (see the link below). Since wave is built using the XView toolkit, all of the resources listed in xview(7) can be used with wave. In addition, the following wave-specific resources may also be set:

Wave.AllowDottedLines
This resource specifies if wave is allowed to render dotted lines. wave normally draws annotation marker bars as dotted lines, and may use dotted lines for other display elements on black-and-white displays for clarity. Some X servers do not properly render dotted lines, however; if you observe irregular or missing annotation marker bars, change the value of this resource from True to False.
Wave.Anntab
This resource specifies the name of a file that contains a table of annotation definitions. The environment variable ANNTAB can also be used to specify this filename; the resource overrides the environment variable if both are set. The file contains one-line entries of the form
15 % Funny looking beat

in which the first field specifies the (numeric) annotation code in the range between 1 and ACMAX inclusive (see /usr/include/wfdb/ecgcodes.h for a list of predefined codes and for the definition of ACMAX); the second field (‘%’ in the example) is a mnemonic (used in annotation display and entry), and the remainder of the entry is a description of the intended use of the annotation code (which appears next to the mnemonic in the ‘Type’ field and menu of ‘Annotation Template’ windows). Lines in the annotation table that begin with ‘#’ are treated as comments and ignored. It is not necessary to specify an annotation table when editing an existing annotation file unless previously undefined annotation types are to be added to it during the editing process, although it is generally harmless to do so.
Wave.Dpi
This resource specifies the display resolution in dots per inch in the form MMxNN, where MM is the horizontal resolution and NN is the vertical resolution. Normally, the resolution is known to the X server, and it is unnecessary to specify this resource. If your X server is misinformed, wave’s calibrated display scales will be incorrect; the best solution is to specify the resolution using a server option such as the -dpi option supported by MIT’s X11 servers, since this will solve problems common to any other applications that require calibrated scales as well. Not all X11 servers support such an option, so this resource is available as a work-around. The command-line option -dpi overrides the resource if both are specified. (If you don’t know the resolution, use xdpyinfo(1) to determine what your X server thinks it is. Then run wave, enable the grid display, and measure the grid squares with a ruler. If they are larger than 5 mm, the number of dots per inch returned by xdpyinfo is too large; adjust the Wave.Dpi resource proportionally, and repeat the process until the grid squares measure 5 mm in each direction.)
Wave.GraphicsMode
This resource specifies the graphics mode used by wave; it can be overridden using the -g, -m, -O, or -S options. The legal values are 1 (monochrome mode), 2 (overlay greyscale mode), 4 (shared color mode), 6 (shared grey mode), and 8 (overlay color mode).
Wave.SignalWindow.{Grey|Color}.Element
These resources specify the colors to be used on greyscale or color displays. The ‘Color.*’ resources are used only if the display is color-capable and neither greyscale nor monochrome mode has been specified. The defaults are:
ElementGreyColor
Backgroundwhitewhite
Gridgrey75grey90
Cursorgrey50orange red
Annotationgrey25yellow green
Signalblackblue
Wave.SignalWindow.Mono.Background
In monochrome mode, the background is normally white, and all other display elements are normally black. The reverse can be obtained by setting this resource to black. (There is at least one server for which this fails.)
Wave.Scope.{Grey|Color}.{Foreground|Background}
These resources specify the colors to be used in the Scope window on greyscale or color displays. The Foreground color is used for the waveform and the time display; by default, it matches the color used for signals in the signal window (see the previous item). Some X servers do not allow the background color of the Scope window to be set, because of the color map animation and stippled erasing techniques used.
Wave.Scope.Mono.Background
This resource can be used to invert the foreground and background of the Scope window when WAVE is running in monochrome mode. This does not work for all X servers.
Wave.SignalWindow.{Height_mm|Width_mm}
These resources specify the preferred dimensions (in millimeters) for the signal window. The defaults are 120 and 250 respectively.
Wave.SignalWindow.Font
This resource specifies the font used to display annotations and time marks in the signal window. The default is fixed.
Wave.TextEditor
This resource specifies the name of the text editor invoked by wave to permit you to edit wave’s log and analysis menu files. The default is textedit (the OpenLook visual editor). You may override this resource by using the environment variable EDITOR, which is also used by many other UNIX applications that invoke editors.

Display options

Initial values for the settings controlled from wave’s View window can be specified using either X resources or command-line options. Once suitable settings have been selected, use the ‘Save as new defaults’ button in wave’s View window to record them in your .Xdefaults file. In this section, the X resource name is specified first, and the command-line option follows.

By default, all of the display options in the first group are off (False); set any of these X resources to True to enable these options, or use the command-line options to do so.

Wave.View.Subtype (-Vs)
Display annotation subtyp fields.
Wave.View.Chan (-Vc)
Display annotation chan fields.
Wave.View.Num (-Vn)
Display annotation num fields.
Wave.View.Aux (-Va)
Display annotation aux fields.
Wave.View.Markers (-Vm)
Display annotation marker bars.
Wave.View.SignalNames (-VN)
Display signal names along the left edge of the signal window.
Wave.View.Baselines (-Vb)
Display baselines for any DC-coupled signals, and label the zero levels and the units along the right edge of the signal window.
Wave.View.Level (-Vl)
While the pointer is in the signal window and any mouse button is depressed, track the intersections of the marker bar with the signals and draw horizontal marker bars across the signal window at the levels of these intersections.

The remaining resources and command-line display options correspond to the menu buttons in wave’s View window. The value of each resource, or the numeric argument that immediately follows the command-line option, should match the position of the desired menu choice, where the top item on each menu is in position 0, the one below it is in position 1, etc. For example, to set the initial amplitude scale to 5 mm/mV (the item at position 2 in the ‘Amplitude scale’ menu), add -Vv 2 to the command line, or Wave.View.AmplitudeScale:2 to the X11 resource database.

Wave.View.TimeScale (-Vt)
Set the time scale (0: 50 mm/min; 1: 125 mm/min; 2: 250 mm/min; 3: 500 mm/min; 4: 12.5 mm/sec; 5: 25 mm/sec (default); 6: 50 mm/sec; 7: 125 mm/sec; 8: 250 mm/sec).
Wave.View.AmplitudeScale (-Vv)
Set the amplitude scale (0: 1 mm/mV; 1: 2.5 mm/mV; 2: 5 mm/mV; 3: 10 mm/mV (default); 4: 20 mm/mV; 5: 40 mm/mV; 6: 100 mm/mV).
Wave.View.SignalMode (-VS)
Set the choice on the ‘Draw’ menu (0: all signals (default); 1: listed signals only).
Wave.View.AnnotationMode (-VA)
Set the choice on the ‘Show annotations’ menu (0: centered (default); 1: attached to signals; 2: as a signal).
Wave.View.TimeMode (-VT)
Set the choice on the ‘Time display’ menu (0: elapsed (default); 1: absolute; 2: in sample intervals).
Wave.View.GridMode (-VG)
Set the choice on the ‘Grid’ menu (0: none; 1: 0.2 s; 2: 0.5 mV; 3: 0.2s x 0.5 mV (default)).

In addition to the usual ways of setting X resources, it is possible to set any of those listed above, as well as any of the generic XView resources, by using the -xrm or -default options on the command line when starting wave. For example, you can set the background color of the signal window using a command such as
   wave -r 100s -xrm Wave.SignalWindow.Color.Background:lightblue

Running Two or More Wave Processes

By specifying two or more record names, separated by ‘+’ characters, in the command-line argument that follows ‘-r’ (see above), you may open separate WAVE signal windows (processes) for each record. These processes are almost completely independent: from any signal window, you may navigate within the record, change display settings, edit annotations, run external analysis programs, quit the process, etc., without affecting any other signal windows.

For example, you may open two signal windows for the same record by:
   wave -r 100+100 -a atr

You can now move about the record freely in either window. This facility makes it easy to compare different segments of the record. Note that whenever two or more windows are displaying the same set of annotations, as in this case, only one should be editing the annotations at any given time.

The window associated with the last record named on the command line has a special status: it is designated the master signal window, and an extra button (labelled ‘Sync’) appears at the top of this window. Clicking on this button causes all of the other signal windows to be redrawn so that the times shown in their lower left corners match that in the master signal window. (Note, however, that if you have quit a signal window from the middle of the list, any signal windows from earlier in the list will no longer respond to sync requests.)

By default, all command-line arguments apply to all signal windows. You may specify an argument that is to apply to only one signal window, however, by prefixing the argument with ‘+n/’, where n is the signal window number. (The first signal window, corresponding to the first record named on the command line, is signal window number 0; the next is number 1, etc.)

This facility has many applications. For example, you may wish to open two copies of the same record, with two different annotators:
   wave -r 100+100 -a +0/atr +1/qrs

In this case, record 100 is opened in two windows, with annotator ‘atr’ in window 0 and annotator ‘qrs’ in window 1. (The ‘-a’ option applies to both windows since it does not have a ‘+n/’ prefix.)

As another example, you may wish to discuss a record with colleagues at other locations:
   wave -r 200+200+200 -a qrs +0/-display +0/atlantic.bigu.edu:0 \

       +1/-display +1/pacific.widget.com:0

Here, record 200 is opened in three windows. Window 0 is opened on display 0 of atlantic.bigu.edu, window 1 on display 0 of pacific.widget.com, and window 2 (the master window) on the local display. (For this to work, your colleagues must first allow your computer to open windows on their displays, typically using xhost. See xview(7) for information about the -display option. Notice that the ‘+n/’ prefix must be attached to both the ‘-display’ option and to its argument in order to apply both of these arguments to the same signal window.) Your colleagues can freely move about the record, but you can direct the discussion at any time by using the Sync button in your signal window. In a case such as this one, anyone can enable editing; you should do so only after making sure that no one else has. Once you have saved your work (by selecting ‘Save’ from the File menu), your changes become visible to your colleagues if they reload the annotations (by clicking on ‘Reload’ from the Load window).

As a final example, the MIMIC Database includes both high-resolution waveform records and medium-resolution (roughly 1 sample per second) computed measurement records. You may view both of these at the same time using a command such as:
   wave -r 237+237n -a all

Typically, you will wish to view the high-resolution and low-resolution data at different time scales. Although wave attempts to choose reasonable defaults, you can adjust the scales independently if you wish:
   wave -r 237+237n -a all +1/-Vt +1/2

If you use wavescript or wave-remote to control the master signal window (this happens by default unless you use the -pid option of these programs to control a different signal window), the other signal windows are kept synchronized with the master window.

Note that you cannot increase the number of signal windows in a group once you have started a wave process group, although you can run more than one process group at a time if you wish.

Menu File

wave uses a simple menu file to allow you to set up analysis options. Each line in the file corresponds to a button in the Analyze window (except for empty lines and lines that begin with ‘#’, which are ignored). Within each line, the syntax is label<tab>action, where <tab> is one or more tab characters. The label field is used to identify a command button in the Analyze window, and the action field is any command acceptable to your shell. button-label and action may include spaces if needed; if necessary, a ‘\’ may be used at the end of a line to indicate that it is continued on the next line. Before the command is executed, wave replaces certain tokens with appropriate strings; these include:

$RECORD
The name of the current record.
$ANNOTATOR
The name of the current input annotator.
$START
The currently selected ‘start analysis’ time.
$END
The currently selected ‘end analysis’ time.
$DURATION
The time interval between $END and $START.
$LEFT
The time corresponding to the left edge of the signal window.
$RIGHT
The time corresponding to the right edge of the signal window.
$WIDTH
The time interval between $RIGHT and LEFT.
$SIGNAL
The currently selected signal number (as shown in the Analyze window).
$SIGNALS
The current signal list (as shown in the Analyze window).
$LOG
The name of the current log file (as shown in the Log window).
$WFDB
The WFDB path (from the Load window).
$WFDBCAL
The name of the WFDB calibration file (from the Load window).
$TSCALE
The time scale, in mm/sec.
$VSCALE
The amplitude scale, in mm/mV.
$DISPMODE
The annotation display mode (0: annotations displayed in center, no marker bars; 1: annotations displayed in center, long marker bars; 2: annotations attached to signals, no bars; 3: annotations attached to signals, short bars; 4: annotations displayed as a signal, no bars; 5: annotations displayed as a signal, long bars)
$PSPRINT
The command for printing PostScript data from the standard input, as specified in the Print Setup window.
$TEXTPRINT
The command for printing text from the standard input, as specified in the Print Setup window.
$URL
The URL specified by the most recently selected link.

Other tokens that begin with ‘$’ are passed to the shell unchanged.

Example

The default menu file includes the following lines (among others):
Mark QRS complexessqrs -r $RECORD -f $START -t $END -s $SIGNAL
Calibratecalsig -r $RECORD -f $START -t $END -s $SIGNALS
Extract segmentsnip -i $RECORD -f $START -t $END -n n_$RECORD \
-a $ANNOTATOR
List annotationsrdann -r $RECORD -a $ANNOTATOR -f $START -t $END
List samplesrdsamp -r $RECORD -f $START -t $END -s $SIGNALS
Print chartecho $RECORD $START-$END | \
pschart -a $ANNOTATOR -g -l -R -s $SIGNALS - | $PSPRINT
Print full disclosureecho $RECORD $START-$END | \
psfd -a $ANNOTATOR -g -l -R -s $SIGNALS - | $PSPRINT

Keyboard Commands

Whenever the pointer is in the signal window, the normal arrow pointer is replaced by a crosshair pointer. At these times, the numeric keypad and several of the function keys may be used for many annotation editing and display operations, and the normal alphanumeric and punctuation keys can be used to select single-character annotation mnemonics (displayed in the Annotation Template window). ‘Num Lock’ must be off if you wish to use the keypad for editing operations. Some of the function and numeric keypad commands work on Sun keyboards only; in these cases, alternate keyboard commands for use with PC and other keyboards are shown in parentheses. Most of these alternate commands also work on Sun keyboards.

<Help> (<F1>)
Open XView spot help for the item under the pointer. (Unlike most of the other keyboard commands, this command is available at any time, not only when the pointer is in the signal window.)
<left arrow>
Select the annotation to the left of the pointer. (Click left to do this using the mouse. These actions also work when the pointer is in the scope window.)
<right arrow>
Select the annotation to the right of the pointer. (Click right to do this using the mouse. These actions also work when the pointer is in the scope window.)
<up arrow> Move the selected annotation up one signal (i.e.,
decrement its chan field). This command works in multi-edit mode only (enter multi-edit mode by choosing ‘attached to signals’ from the ‘Show annotations’ menu in wave’s View window).
<down arrow>
Move the selected annotation down one signal (i.e., increment its chan field). This command works in multi-edit mode only.
keypad <5> (<F2>)
Insert an annotation at the current position of the pointer. (Click the middle button to do this using the mouse. Annotation editing must be enabled for this action to be successful.)
keypad <=> (<F3>)
Move the pointer toward the left.
keypad <*> (<F4>)
Move the pointer toward the right.
<Copy> (<F6>)
Copy the selected annotation to the Annotation Template.
<Find> (<F9>)
Search forward.
<ctrl><Find> (<ctrl><F9>)
Search backward.
<End> (<shift><F9>)
Advance to the end of the record.
<Home> (<ctrl><shift><F9>)
Move to the beginning of the record.
<PgDn> (<F10>)
Advance half a screen.
<ctrl><PgDn> (<ctrl><F10>)
Advance a full screen.
<PgUp> (<shift><F10>)
Move back half a screen.
<ctrl><PgUp> (<ctrl><shift><F10>)
Move back a full screen.
<Enter> (<Return>)
(Only if a link annotation has been selected.) Show the external data specified by the link using a Web browser; start the Web browser first if necessary.

Bugs

Under SunOS, once you have opened the Analyze window or have selected Print from the File menu, do not attempt to suspend wave (for example, by typing control-Z in the controlling terminal window). Under these circumstances, wave may exit immediately (without quit confirmation) and any unsaved edits may be lost. This problem is the result of a bug in the XView termsw package used for the Analysis Commands window. To avoid this bug, always run wave in the background under SunOS. The Linux, Mac OS X, MS Windows, and Solaris 2.x versions of the XView library do not have this bug.

If wave opens with an empty signal window, this may mean that the X server’s backing store is disabled. wave versions 6.8 and later incorporate a workaround that avoids this problem. If you must use an earlier version of wave, enable backing store and restart the X server. (Using the X servers from the x.org or XFree86 projects, backing store can be enabled by inserting the line ‘Option "backingstore"’ in the ‘Device’ section(s) of the xorg.conf or XF86Config-4 file. If your X server is normally started by a display manager such as xdm, close all windows and restart the server with <ctrl><alt><backspace>. Otherwise, log out, log in, and restart the X server manually if necessary.)

If this doesn’t solve the problem, use any of wave’s navigation controls, or resize the signal window, to make the signals visible. On some 24-bit displays, this problem may be the result of an X server bug, and these methods will work around the problem. On some of these displays, text in the signal window may be invisible using overlay graphics mode; if this happens, use the -S option.

No more than one piped record (see the WFDB Programmer’s Guide) can be viewed in a single invocation of wave. If the signal file is a pipe, it is possible only to search forward through it (although wave caches several of the most recently displayed windows, which can be reviewed in any case). Using the ‘>’ button to move by half a frame does not work properly with piped input, nor does changing the display scales, since these actions require rereading the signals.

There appears to be a subtle incompatibility between XView-based applications such as wave and at least some X servers. The symptom of this problem is that wave’s View panel may be blank, and many warning messages from the notifier may appear in the controlling terminal window. This problem appears to occur only when all of the following are true: the X server is running on a multi-head display with Xinerama enabled, the user does not have root privileges, a .Xdefaults file exists, and wave or another XView application has run at least once since the X server was started.

A more serious incompatibility (which may be related to the subtle incompatibility noted above) appeared with the release in 2009 of the X.org version 1.6.3 X server, which freezes when any application that uses the XView library (such as wave) ’grabs’ the mouse pointer. By default, XView applications do so in response to a left button click on any XView control. ’Grabs’ can be disabled, and this behavior avoided, by using the -Wfsdb option available in wave and in other XView applications. In wave version 6.10 and later versions, the default behavior of XView has been changed to disable ’grabs’, and this problem does not occur.

See Also

pschart(1) , xview(7)
WAVE User’s Guide (http://www.physionet.org/physiotools/wug/)
X Window System User’s Guide: Open Look Edition (http://www.oreilly.com/openbook/openlook/)

Availability

wave currently runs under FreeBSD, GNU/Linux, Mac OS X, MS-Windows with Cygwin/X, Solaris, and SunOS. It should be easily portable to any POSIX-compliant OS that can support X11 and XView. If you would like to use wave on a system other than those listed above, you will need to port XView to your system first (or purchase a commercial port if one is available). Sources for XView are available from PhysioNet (www.physionet.org, where the sources for wave itself are also available), www.ibiblio.org, and their mirrors. We cannot offer assistance in porting XView; if you wish to try this, you are on your own. If you successfully port the cmdtool terminal emulator application included in the XView sources, we will assist you in porting wave (this is much simpler than the XView port).

Author

George B. Moody (george@mit.edu)

Sources

http://www.physionet.org/physiotools/wfdb/wave/


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