WFDB quick start for MS-Windows 95/98/NT/2000/ME/XP/Vista/7

Under Windows Vista or Windows 7, it may be necessary to perform some or all of the steps below while logged into an account with "administrator" permissions.

1. Install Cygwin in a location that does not have any spaces in its pathname. The default and preferred location is c:\cygwin. Do not use locations under Program Files, Documents and Settings, or any other directory containing a space in its name. Be sure to leave the "Default Text File Type" as "Unix" (not "DOS"), and be sure to select and install the curl-devel, diffutils, gcc, gcc-mingw, make, openssl-devel, sunrpc, libX11-devel, and X-start-menu-icons packages (these are not installed by default in a minimal Cygwin installation).
   
   
2. Install an HTTP client library (optional). If you installed curl-devel together with Cygwin as specified above, you may go on to step 3. Otherwise, install libcurl or libwww now.
   • You will be able to use the WFDB software to read files on local disk drives and CD-ROMs whether or not you install one of these libraries.
   • Direct access from WFDB applications to data files on remote web and FTP servers (NETFILES) is possible only if you install libcurl or libwww.
   • Direct access from WFDB applications to password-protected data files on remote web and FTP servers requires libcurl 7.12.0 or later.
   • If you skip this step now, you may install libcurl or libwww and recompile the WFDB library later to enable NETFILES access for all of your WFDB applications. It will not be necessary to recompile the applications themselves.
   
   
3. Install XView (optional).
   • You will not be able to compile or use WAVE unless you have installed libX11-devel (in step 1 above) and XView, but none of the other WFDB applications require these packages. Other components of PhysioToolkit, such as plt and SEMIA, require X11 and XView.
   • Add /usr/openwin/bin (or the directory containing textedit, if you have a non-standard installation of XView) to your PATH before attempting to compile WAVE. (See the instructions here.)
   
   
4. Download the current version of the WFDB software package as sources or binaries. Binary packages are provided as a convenience and may not be up-to-date; we strongly recommend following the procedure described below for compiling the software from the sources instead. If you plan to compile WFDB applications that are not included in the binary package, please start with the sources, and read the note below.

   If you download the sources (recommended):

   • Choose a working directory for the installation. This directory must not have any spaces in its pathname. If your Windows username has no spaces, you can use your Cygwin home directory (c:\cygwin\home\username); otherwise, create a directory beneath c:\cygwin (for example, c:\cygwin\home\wfdb) and use that as your working directory. Save the archive of sources (wfdb.tar.gz) in this working directory.
   • Open a Cygwin terminal emulator window. To open a Cygwin window, either click on the Cygwin desktop icon, or find and run c:\cygwin\cygwin.bat. Under Vista or Windows 7, right-click on the Cygwin icon and choose "Run as administrator" (thanks to Albert Titus for this tip). By default, the current directory within the Cygwin window will be c:\cygwin\home\username initially. If you chose a different working directory, enter that directory by typing a command such as

     cd /home/wfdb
     

     (Omit c:\cygwin\ from this cd command, and use a forward slash (/) rather than a backslash (\) as a directory separator where needed.) Perform the remainder of the installation by typing the commands as shown below into this Cygwin window. Do not use an MS-DOS window for this purpose.
   • Unpack the archive of sources (using tar, included with Cygwin):

     tar xfvz wfdb.tar.gz
     

     If your browser decompressed the archive during the download, you will need to use this command instead:

     tar xfv wfdb.tar
     

     This creates a directory with a name of the form wfdb-10.m.n within your working directory. Look at the list of files printed by the tar command to determine the name of the directory for the next step.
   • Enter this directory and configure the package:

     cd wfdb-10.m.n
     ./configure
     

     (In the cd command, replace wfdb-10.m.n with the name of the directory as printed by tar in the previous step.)
   • (Optional) Compile and test the package without disturbing any previous WFDB installation:

     make
     

     Skip this step on an initial installation. The checks performed by 'make check' (described below) are run on the test binaries if you do perform this step.
   • Compile and install the package (as noted above, installation may require "administrator" permissions):

     make install
     

   • The binaries will be installed in /usr/bin (accessible from outside the Cygwin environment as c:\cygwin\usr\bin). Be sure that this bin directory is in your PATH.
   • (Optional) Check that the WFDB library and applications have been correctly compiled and installed:

     make check
     

     This step compiles a short program that exercises the WFDB library, prints a summary of test results, and prompts you to press <Enter>. After you have done so, the WFDB applications are tested. The tests are very short (typically less than a second each), except that the last one (xform using NETFILES) may take up to a minute if you have a slow or inoperative Internet connection. If any application test fails, its output can be found in the checkpkg subdirectory of the WFDB source tree; compare this output with the files of the same names that can be found in the checkpkg/expected subdirectory.
   • Make the WFDB library available for other applications:

     ln -sf /usr/bin/libwfdb.dll.a /usr/lib
     

   
   If you download the binaries (not recommended):
   • Copy cygwfdb*dll and all of the *.exe files from the directory of MS-Windows binaries into a directory in your PATH. If you have not installed Cygwin (especially not recommended), also copy the other cyg*.dll files from the directory of MS-Windows binaries into the same directory as the *.exe files. Note: you must install Cygwin and Xview in order to use WAVE.
   
   
5. If XView is installed, test WAVE by starting the Cygwin X server and then running (in an xterm window, such as the one that opens when you start the X server) the command:

   wave -r mitdb/200 -a atr
   

   Note that WAVE's menus (marked with a ) are opened using a right click. Annotation editing requires the use of the middle button; if your mouse has only two buttons, you may be able to simulate a middle button click by "chording" (press both buttons at the same time, then release them; see this note for details if necessary).

   If you have not used WAVE before, you may want to follow through the tutorial material in the beginning of the WAVE User's Guide.
   
   

6. Read the manuals. Really! :-) If you want to write your own software to work with PhysioBank data, begin with the WFDB Programmer's Guide. To learn about the wide variety of existing software that can be used to study PhysioBank data, read the WFDB Applications Guide and the WAVE User's Guide.

If you wish to compile your own WFDB applications, or others that are not available in binary format, please begin by compiling and installing the WFDB software package sources, as described above. Once you have done so, copy app/Makefile (a text file contained in the WFDB source package) to the directory that contains the source for the application you wish to compile. Note that app/Makefile is customized based on the installation choices that you make when you run ./configure before compiling the WFDB software package, so it's important to copy the customized version of this file from your copy of the WFDB sources only after running ./configure.

If the application is contained in a single source file (for example, myprogram.c) in the same directory as this customized Makefile, you can compile it and link it with the WFDB library using a command such as

make myprogram

If you need to compile an application contained in several source files, use the command generated by make for a single source file compilation and replace the single source name with those of your multiple source files, separated by spaces. Note that the output file name (the argument of gcc's -o option) should not include the .exe suffix.

The WFDB Software Package also includes wfdb-config, a tiny application that helps to construct gcc command lines without using make. Study the example in wfdb-config(1) to see how to use it.

Making a native Windows version of the WFDB library

The procedure above generates a WFDB library that depends upon Cygwin's POSIX emulation library (cygwin1.dll) to provide a Unix-like operating environment, thus assuring that WFDB applications will behave on MS-Windows as much as possible like they do on other platforms. It is also possible, though not generally recommended, to make a WFDB library that depends only on the native libraries provided with MS-Windows.

There are two specific cases in which you might need a native Windows version of the WFDB library:

• To use the WFDB_tools wrappers with Matlab R14 (but not R13)
• To link the WFDB library to other code that must also be linked with Windows native libraries

The method outlined below will allow you to create a Windows native version of the WFDB library that does not depend on Cygwin's POSIX emulation library or any third party libraries other than those provided with MS-Windows. This method also creates a mostly complete set of WFDB applications (except for WAVE) that are used to test the WFDB library; use them at your own risk, since they may not behave in exactly the same way as the standard versions of the same applications.

Please note that this method, and any others that do not use an ANSI/ISO C compiler such as gcc, are unsupported. Your feedback is welcome, but we do not use any commercial compilers and cannot help you learn how to use them.

1. First perform a standard WFDB installation from sources as described above.
2. (Continue using a Cygwin (terminal emulator) window throughout the steps below.) Select a target directory for the native Windows WFDB installation. We recommend keeping this separate from the standard Cygwin directories to avoid confusion. A good choice is /opt/wfdb. Create a bin subdirectory for the native Windows binaries within this target directory, and add it to your PATH:

   mkdir -p /opt/wfdb/bin
   export PATH="/opt/wfdb/bin:$PATH"
   

   The mkdir command also creates /opt and /opt/wfdb if they do not exist already.
3. (Optional; see README.NETFILES for further information.) Install a native windows version of libcurl:
   1. Download the no-SSL libcurl binary package for Win32 from http://curl.haxx.se/download/ and move the zip file into your (Cygwin) home directory. As of August 2009, the most recent version of this file was libcurl-7.17.1-win32-nossl.zip. (The SSL and SSL+SSPI enabled versions of libcurl should also work if the additional libraries they need are installed, but this has not been tested. The WFDB library does not require SSL or SSPI support.)
   2. Unpack libcurl into /opt:

      cd /opt
      unzip ~/libcurl-*nossl.zip
      

      The libcurl files will unpack into a version-numbered directory under /opt, such as /opt/libcurl-7.17.1. Copy the needed files into /opt/wfdb:

      cd /opt/libcurl-7.17.1
      cp -p bin/curl-config lib/* /opt/wfdb/bin
      cp -pr include /opt/wfdb
      

   3. Using your favorite text editor, edit /opt/wfdb/bin/curl-config, replacing

      prefix=/usr/local
      

      with

      prefix=/opt/wfdb
      

      Also, search for any lines containing '-L/home/dast/src/win32'. Delete this string, and anything that follows it on the same line, wherever it appears. For example, a line that looks like:

      echo ${CURLLIBDIR}-lcurl -L/home/dast/src/win32 ...
      

      should be changed to:

      echo ${CURLLIBDIR}-lcurl
      

      (deleting the remainder of the line following '-lcurl').
4. Enter the top-level directory of the WFDB Software Package (the directory that contains the configure script).

   If you installed libcurl in step 3 above, type:

   make clean
   ./configure --without-cygwin --prefix=/opt/wfdb
   make install
   

   replacing /opt/wfdb with the name of the target directory you chose in step 2 above, if different.

   If you did not install libcurl in step 3 above, type these commands instead:

   make clean
   ./configure --without-cygwin --without-netfiles --prefix=/opt/wfdb
   make install
   

5. Note: If you run

   make check
   

   many checks will fail because text files written by the native Windows WFDB applications will be in DOS format (with CR+LF line terminators). This is normal and is not an indication of problems.

For additional information about this procedure, see README.WINDOWS.

Using a compiler other than gcc

This is strongly discouraged. gcc is free, is of very high quality, and is supported; if you use another compiler, you are on your own. Note that if you compile the WFDB library and applications with gcc, you may link code compiled with another compiler to the WFDB DLL generated by gcc (the DLL is in the same format as that produced by other compilers that generate MS-Windows DLLs).

It is not possible to compile or use WAVE under MS-Windows except by using Cygwin gcc and the Cygwin X libraries.

If you do not use gcc, you must do one of the following:

• Use your compiler in ANSI/ISO C mode if this is supported (see your compiler documentation), or
• Define the symbol MSDOS (to any value) when compiling the WFDB Software Package.

If you do neither of these steps, your compiler will generate a defective WFDB DLL that assumes that files are always opened in so-called text mode, resulting in errors when reading and writing signal and annotation files (which are binary files). You can check to see if this has happened by running the command

    rdsamp -r 100s

     21596	  982	  995
     21597	  978	  989
     21598	  975	  988
     21599	  975	  989

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Updated Tuesday, 13-Oct-2009 14:53:08 EDT