from PhysioNet, the research resource for complex physiologic signals


WFDB quick start for Mac OS X (Darwin)

To install and use the WFDB Software Package successfully, you must know how to use the Terminal application and the Unix shell. If you are unfamiliar with Unix commands, please find and study a good reference on the subject, such as David Pogue's Mac OS X: The Missing Manual, or Dave Taylor's Learning Unix for Mac OS X (both published by O'Reilly), or get the help of a local expert.

The WFDB Software Package has been successfully compiled and tested on Intel-based Macs under Mac OS X 10.6 (Snow Leopard) and 10.5 (Leopard), and on PPC-based Macs under Mac OS X 10.3 (Panther) and 10.2 (Jaguar). We have not tested other versions of OS X. Note that the XView toolkit needed in order to use WAVE is available for PPC but not (yet) for Intel-based Macs.

Thanks to Isaac Henry for the original port of the WFDB Software Package to Mac OS X; to David T. Linker, MD, of the University of Washington, for providing instructions for compiling WAVE under Mac OS X 10.2 on PPC Macs; and to Prof. Logan Donaldson, of York University (Toronto), for the port of the XView toolkit to Mac OS X 10.0 (PPC) that made David's port of WAVE possible.

  1. Install XCode, including "UNIX Development Support". XCode is a set of software development tools including gcc, make, the libcurl and X11 SDKs, and much more. XCode is included on current Mac OS X CDs and DVDs, and can also be freely downloaded from http://developer.apple.com/tools/xcode/.

    If you have installed XCode 4 or later, see this note.

  2. Open a Terminal (or xterm) window. Type the commands shown in the remaining steps below into this window.

  3. Install XView (optional).
    • You will not be able to compile or use WAVE unless you have installed XView, but none of the other WFDB applications requires XView. Other components of PhysioToolkit, such as SEMIA, require XView.
    • At this time, it is necessary to use the XView binaries available here, which work only on PPC-based Macs. A package for Intel-based Macs may be available soon. Sources are available here, but compiling them under Mac OS X is not straightforward.
    • The currently available version does not include the textedit application, which is WAVE's default menu editor. This will not prevent you from using WAVE, but you should set the EDITOR environment variable to the pathname of your preferred text editor before running WAVE if you plan to edit WAVE's menu file. For example, you might add
      export EDITOR=/usr/bin/emacs
      
      to the file named .bash_profile in your home directory.

  4. Download the current version of the WFDB Software Package as sources or binaries. The binary distribution is experimental 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 packages, please start with the sources.

    If you download the sources (recommended):

    • If your web browser decompressed the archive (Safari does this), use this command to unpack it:
      tar xfv wfdb.tar
      
      Otherwise, decompress and unpack with this command:
      tar xfvz wfdb.tar.gz
      

      Unpacking the archive creates a directory with a name of the form wfdb-10.m.n. Enter this directory:

      cd wfdb-10.m.n
      
    • If you are using an unpatched version of XCode 4 or later, edit conf/darwin.def and conf/darwin-slib.def, removing the string '-arch ppc' from the end of the definition of CFLAG in each file. (Read about alternatives below.)
    • Configure and install the package:
      ./configure
      sudo make install
      
      The sudo command prompts for your password, needed in order to install the package in subdirectories of /usr. If you do not have administrative permissions, you may install the package in any writable directory by running make directly, adding an appropriate option:
      make install WFDBROOT=/path/to/another/directory
      
      Note that in this case you will need to add WFDBROOT/bin to your PATH, and WFDBROOT/lib to your DYLD_LIBRARY_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.

    If you download the binaries (not recommended):
    • Download the appropriate binary archive for your CPU type (Intel or PPC). Unpacking the archive creates a directory with a name of the form wfdb-10.m.n-cputype-Darwin. Copy its contents into the same-named subdirectories of /usr:
      cd wfdb-10.m.n-cputype-Darwin
      sudo cp -pr . /usr
      
  5. If XView is installed, test WAVE.
    • On Mac OS X 10.5 and later:
      The X server starts automatically when needed, so simply run the command:
      wave -r mitdb/200 -a atr
      
    • On earlier versions of Mac OS X:
      Unless the X server is running already and an xterm window is open, run the command:
      startx &
      
      In the xterm window, type the command:
      wave -r mitdb/200 -a atr
      

    Note that WAVE's menus (marked with a nabla) are opened using a right click; if you have a one-button mouse, simulate a right click by pressing and holding the apple key while clicking. Annotation editing requires the use of the middle button, which can be simulated by using the option key while clicking.

    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.

XCode 4 and PPC architecture

The WFDB Software Package supports creation of multi-architecture ("fat") binaries that run on 32- and 64-bit Intel as well as PPC versions of Mac OS X, using XCode 3 and earlier versions based on the gcc C compiler. In XCode 4, Apple replaced gcc with its own C compiler, breaking support for its older PPC machines. As a result, you will need to choose one of these options before compiling the WFDB Software Package, if XCode 4 is installed on your computer: