setwfdb, cshsetwfdb - set WFDB environment variables
. setwfdb
source cshsetwfdb
call setwfdb
WFDB applications search for input files by looking
for them in an ordered list of locations called the WFDB path. These locations
can be given by directory names or (if the WFDB library has been installed
with NETFILES support) URLs. If the WFDB environment variable is set, its
value specifies the WFDB path; otherwise, applications use the builtin
default path specified at the time the WFDB library was compiled. The default
path (DEFWFDB, defined in the WFDB library source file wfdblib.h) includes
the current directory (‘‘.’’), the system-wide database directory installed as
part of the WFDB Software Package (usually /usr/database), and the PhysioBank
data archive (http://www.physionet.org/physiobank/database).
WFDB applications
that need access to the signal calibration database find it in a file located
on the WFDB path. If the WFDBCAL environment variable has been set, its
value specifies the name of the calibration file; otherwise, applications
look for the default calibration file, the name of which (wfdbcal) is compiled
into the WFDB library.
Many users will not need to change the defaults,
but for those who do, the scripts described here may be helpful. Important:
these programs must be customized before using them for the first time
on a new machine. Since they are text files, use any text editor to customize
them.
setwfdb sets the environment variables WFDB
and WFDBCAL. It must be executed using the ‘‘.’’ as shown above. It may be convenient
to include an invocation of setwfdb in your .profile file.
cshsetwfdb
sets WFDB and WFDBCAL similarly for the C-shell. It must be executed using
‘‘source’’ as shown above. It may be convenient to include this command in
your .cshrc file.
- WFDB
- The database path: a list of directories
that contain database files. An empty component is taken to refer to the
current directory. All applications built with the wfdb(3)
library search
for their database input files in the order specified by WFDB. If WFDB
is not set, searches are limited to the builtin WFDB path (see above).
Under Unix, directory names are separated by colons (:), and the format
of WFDB is that of the Bourne shell’s PATH variable (see sh(1)
). Under MS-DOS,
directory names are separated by semicolons (;), and the format of WFDB
is that of the MS-DOS PATH variable (colons may be used following drive
specifiers within WFDB in this case). MacOS does not support environment
variables as such; under MacOS, the builtin WFDB path is defined in fdblib.h
as described above, and it contains a semicolon-delimited list of directories
(folders) as under MS-DOS, but with colons used as directory separators
rather than backslashes as under MS-DOS. Alternatively, whitespace can be
used (under any environment) to separate components of the WFDB path. Under
any environment, if the value of WFDB begins with ‘@’, the remainder of the
string is taken as the name of an ‘‘indirect WFDB path file’’ that defines
the database path in the format described above. This feature was introduced
in WFDB library version 8.0, mainly to permit
MacOS users to modify the WFDB path without recompiling the WFDB library,
but it is also useful under MS-DOS to avoid the 128-character limit on the
length of environment variables. Indirect WFDB path files can be nested
up to 10 levels deep.
- WFDBCAL
- The name of the WFDB calibration file (see
wfdbcal(5)
). The usual rules for finding WFDB files by searching the WFDB
path apply to the WFDB calibration file, so the value of WFDBCAL need not
be an absolute path name. The WFDB calibration file is used by WFDB applications
that need to plot signals at standard scales, as well as by calsig(1)
,
which can determine the baseline and gain of signals if calibration pulses
are present and if the parameters of the calibration pulses are described
in the calibration file. If WFDBCAL is not set by the user, the WFDB library
uses a default WFDB calibration file (wfdbcal, named in wfdblib.h). If the
WFDB calibration file is not readable, programs that rely on it may not
choose appropriate scales for some types of signals.
George B. Moody
(george@mit.edu)
Note that these are templates and will need to be
customized before use:
http://www.physionet.org/physiotools/wfdb/app/setwfdb
http://www.physionet.org/physiotools/wfdb/app/cshsetwfdb
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