Editing the result

In the previous chapter we were able to detect the QRS complexes of a recording created by a commercial equipment by using WFDB tools. Now we want to edit the result.

The whole picture

To do this, we need a viewer that allows deleting or adding QRS detections as well as reposition them if necessary. First of all, we are going to show the result, then we will explain the choices taken, as well as the process of installation. Once installed, the command is direct:

 
[j@localhost Code]$ wave -r ecg -a qrs

We indicate the record name (ecg) as well the annotation file qrs and a nice window appears. The result (sligthly modified) can be seen in the figure 3.1

Figure 3.1: Wave showing the result of sqrs on our file

The result of the analysis seems very good. Let me stress that the signal is not good at all and that it was not even an WFDB signal in origin. Probably, no editing is necessary. In any case, editing the annotations with wave is a pleasure. Many subtle features are included (from defining your own set of annotations to measuring signal amplitudes, from acting as an interface to other programs to synchronizing several windows, from directly accessing recordings on the PhysioNet web server to annotating a recording from scratch). It is a wonderful program. You can follow an excellent tutorial at PhysioNet with the details. Wave is installed as a part of WFDB Software Package in Linux systems.

Differences between Gtkwave and Wave

At this point, given the importance of wave, I am going to dedicate some time to installation topics. Firstly, I will emphasize the differences between wave and gtkwave.

To develop a graphic program, you usually use a graphic library. A graphic library is a set of graphic functions that do things such as creating a window, drawing a line etc. Wave uses XView. Since it is not easy to use it in Windows, there is an alternative. A similar program (Gtkwave) also developed by the authors of WFDB uses Gtk. Since both programs are more or less similar, I will stress the differences:

• Gtkwave is easier to install than Wave in Linux
• Gtkwave can be used in Windows. Wave can not be used in Windows

If you want to run WFDB in Windows, then you can download the Self-extracting-installer. It installs a set of WFDB tools as well as Gtkwave. The installation is very easy and you can immediately use the program with the recording 100s that is included in the package.

If you are using Linux, I strongly recommend the use of Wave (instead of Gtkwave). Let me detail some reasons:

• The documentation is more precise
• There are some very nice features such as the ``scope window'' not implemented in gtkwave
• At least in Windows 98 and Windows NT, to mark the signal you often need to use the key F2. Sometimes this key does not act and the control is lost. This often happens when you use the mouse to navigate through the record. (If you want to do it and find this problem, try to navigate using Page Up Key and Page Down Key).
• There seems to be a bug when you select viewing only some signals in gtkwave (e.g., calling it with option -s and selecting listed signals only) drawing always the first signal when you do not select drawing all signals.
• In the annotation template window, the list of type usually exceeds the size of the screen, making difficult the selection of some options
• Wave is in general more stable

I would not like to be misunderstood. Gtkwave is an excellent program. Wave is even better. If you are running Linux, I recommend that you make the aditional effort of installing wave.

In any case, if you are running Windows and you feel frustrated by not being able to use wave, turn a lemon into lemonade: install Linux.

Installation in Mandrake 9.0

Since the main inconvenience encountered with Wave is the difficulty in the installation, and the details in PhysioNet are directed to Red Hat, I will try to detail the procedure in Mandrake 9.0. Everything you need is included in the distribution except:

• WFDB package. It can be downloaded in RPM form from here in PhysioNet. You can download the binary WFDB RPM by clicking in the paragraph entitled Installing the WFDB Software Package from a binary RPM.
• XView library. On PhysioNet, there are different libraries for several versions of Red Hat. With Mandrake 9.0 the version of Red Hat 7.0 functions properly. You can download these RPMs here.

And now the procedure:

• Installation of the W3C libwww libraries.You can install them from Mandrake disks. You need to install the packages w3c-libwww and w3c-libwww-devel. You can do it by accessing Mandrake Control Center Software Management and Install Software. In this way every dependency will be solved.
• Installation of XView libraries. Install in this order xview-3.2p1.4-16.i386.rpm, xview-devel-3.2p1.4-16.i386.rpm and xview-clients-3.2p1.4-16.i386.rpm. An easy way to do this is opening the file with kpackage (by clicking on the icon of the file, once you downloaded it to your disk) and following the instructions to install the package. If the order is not the appropriate, kpackage will require you to install the other needed packages
• Installation the WFDB package. You can install wfdb-10.3.0-1.i386.rpm by using kpackage in the same way that in the previous point.

XView uses an editor called textedit (included in xview-clients). It is installed in /usr/openwin/bin/textedit. To call it from Wave, it is necessary to define it as EDITOR

 
[j@localhost Code]$ export EDITOR=/usr/openwin/bin/textedit
[j@localhost Code]$ wave -r ecg -a qrs

Some alternatives are to add /usr/openwin/bin to your PATH, or to copy textedit into a directory in your PATH, or to make a link from /usr/openwin/bin/textedit to a directory in your PATH; if you do any of these it will not be necessary to set EDITOR each time you plan to use 'textedit' within 'wave'.

Once made this arrangements, when you push the button Analyze and then Edit Menu you are asked to copy wavemenu in your own directory. Once you click on copy the menu (a very useful resource) appears edited with textedit. You can define any other editor (not necessarily textedit) to edit the menu.

Finally, when you press F1 in wave, nothing happens. To get help when you press F1, you can use the next command.

 
[j@localhost Code]$ xmodmap  -e "keysym F1 = Help"
[j@localhost Code]$ wave -r ecg -a qrs

Now, when you press F1 a help window appears.

At this moment we have installed Wave. It is time to enjoy it. If you are connected to the Internet and you type the command

 
[j@localhost Code]$ wave -r slpdb/slp01a -a st

then you have access to the record slp01a of the database slpdb with the annotation st, as if it had been downloaded to your computer. It is a sleep recording with a quantification of stages in epochs of 30 seconds. Believe or not, you can navigate through it from your own computer without downloading the recording.

Let's do the same with our recording:

 
[j@localhost Code]$ wave -r ecg -a qrs

And we can begin to practice with our own data.

In summary

It has been a long and challenging session. At this moment we have installed wave. We can follow the tutorial and edit our results. We can add or eliminate annotations, we can change the type of annotation or assign them to some specific signal. Once finished we will export the results to continue our analysis.

In the next chapter we are going to use Scilab to analyze the data.