WFDB quick start for FreeBSD

Special thanks to Giuseppe Pagnoni for his notes, on which these are based. Any errors are mine, not his! -- GBM
  1. Install gcc (requires root permissions) if it is not installed already (try the command 'gcc --version' to check).

  2. Install an HTTP client library (optional, requires root permissions). If neither libcurl nor libwww has been installed already, install one of them 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, requires root permissions).

    • You will not be able to compile or use WAVE unless you have installed the X11 developer's toolkit, including /usr/include/X11/*.h, and XView, but none of the other applications require XView. Other components of PhysioToolkit, such as plt and SEMIA, require X11 and XView.
    • Unless you have compiled and installed XView from sources, install textedit from the FreeBSD Project (textedit is not included in the FreeBSD port of XView).
    • Add /usr/X11R6/bin (or the directory containing textedit, if you have a non-standard installation of XView) to your PATH before attempting to compile WAVE.
  4. Download the current version of the WFDB software package as sources.

    • Unpack the archive of sources:

      tar xfvz wfdb.tar.gz

      This creates a directory with a name of the form wfdb-10.m.n.

    • Enter this directory, configure, and install the package:

      cd wfdb-10.m.n
      make install

      The make command requires root permissions, and installs the package in subdirectories of /usr. If you do not have root permissions, you may install the package in any writable directory by adding an appropriate option to the make command above:

      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 LD_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.

  5. If XView is installed, test WAVE with the command:

    wave -r mitdb/200 -a atr

    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.

Questions and Comments

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Updated Thursday, 09-Jul-2015 17:04:18 CEST

PhysioNet is supported by the National Institute of General Medical Sciences (NIGMS) and the National Institute of Biomedical Imaging and Bioengineering (NIBIB) under NIH grant number 2R01GM104987-09.