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Introduction

Most of this guide consists of UNIX man pages that describe the applications included in the WFDB (Waveform Database) Software Package (and related software from PhysioToolkit). This introduction contains important information about how to interpret the material in the main sections of the guide, and about common conventions for using all of the WFDB applications that are not described in the main sections. The FAQ contains additional information that will be particularly helpful if you are using MS-Windows (but it may be of interest even if you are not).

Using this Guide

The organization follows the traditional arrangement of the UNIX Reference Manual: section 1 contains programs, section 3 contains libraries, and section 5 contains file formats. In the UNIX Reference Manual, sections 2 and 4 are reserved for system calls and device interfaces respectively; these sections do not exist in this guide. Following convention, a citation such as rdann(1) refers to the page titled rdann in section 1 of this guide.

A man "page" may span more than one physical page, although most do not. Each man page in section 1 of this guide documents one or more applications, as indicated in the NAME section at the top. The SYNOPSIS appears next; it illustrates the form of the command line needed to run the application. In the synopsis, boldface indicates text to be typed as is, and italics indicate replaceable arguments; brackets ([], which are not to be typed) surround arguments that may be omitted, and ellipses (...) follow arguments that can be repeated. The DESCRIPTION sections are intentionally terse; this is a reference manual and not a tutorial introduction to the software described within. In those cases for which relevant tutorial material exists elsewhere, references appear in the SEE ALSO sections of each man page. A unique feature of this guide is the SOURCE section at the end of each page, which provides a URL where you may find the current version of the source(s) for each application.

Under GNU/Linux, Mac OS X, or UNIX, if the WFDB Software Package has been installed on your system, you can also access the information contained in the main sections of this guide using man and related programs. For example, to see the manual page for rdsamp, run the command

	man rdsamp
(This also works under MS-Windows if you have installed the Cygwin package, which includes the man utility for formatting and reading manual pages.) In some cases you may need to add /usr/local/man to your MANPATH environment variable, in order to make these pages accessible to man.

Using WFDB Applications

If you have not used any of these programs before, you may need to set up your environment properly so that WFDB applications can find their input files. See setwfdb(1) for information about doing this; a more detailed discussion may be found in the first chapter of the WFDB Programmer's Guide, in the section about the database path. Most users will not need to do this, however.

Certain types of command arguments are used by many of the applications described in this guide. These include:

record
Where this appears, substitute the name of a WFDB record. A record name is not a file name! The first part of the name of a .hea file is the name of the record to which the .hea file belongs; so the record name corresponding to 100.hea is 100. For example, MIT-BIH Arrhythmia Database record names are 3-digit numbers, AHA Database record names are 4-digit numbers, and European ST-T Database record names begin with lowercase `e', followed by a 4-digit number. Record names may contain letters, digits, and underscores. Case is significant in record names that contain letters, even in environments such as MS-Windows for which case translation is normally performed by the operating system on file names; thus `e0104' is the name of a record found in the European ST-T Database, whereas `E0104' is not. Once again: a record name is not a file name; record names never include an extension (.hea, .dat, etc.).

Wherever a record name can be supplied to a WFDB application, you may include path information if necessary. For example, if the WFDB path includes the current directory, and if the current directory includes a subdirectory named my_records, and if that directory contains a record named record_23, you can supply my_records/record_23 as a record argument. See the WFDB Programmer's Guide for further details on record names.

Each PhysioBank database directory includes a text file named RECORDS, which lists the record names for all records in that directory.

annotator
Where this appears, substitute an annotator name. Annotator names are not file names! The suffix (extension) of the name of an annotation file is the annotator name for that file; so, for example, the annotator name for `e0104.atr' is `atr'. The special annotator name `atr' is used to name the set of reference annotations supplied by the database developers. Other annotation sets have annotator names that may contain letters, digits, and underscores, as for record names.

Each PhysioBank database directory includes a text file named ANNOTATORS, which lists the annotator names for all annotation files in that directory.

time
Where this appears, substitute a string in standard time format. Time arguments generally specify elapsed times from the beginning of the record (for exceptions to this rule, see the section on the strtim function in the WFDB Programmer's Guide). Examples of standard time format:
2:14.875   2 minutes + 14.875 seconds
143143 seconds (2 minutes + 23 seconds)
4:02:014 hours + 2 minutes + 1 second
4:2:1same as above
s1234512345 sample intervals
etime of the end of the record
signal
Where this appears, substitute a signal number or (in most cases) a signal name. Signal numbers are integers; the first signal in each record is signal 0. In printed documentation for the databases, signals always appear with signal 0 at the top, signal 1 beneath, etc. Signal names are the strings printed by signame(1).
signal-list
Where this (or signal ...) appears, you may specify more than one signal number in any desired order; separate the signal numbers or names using spaces. Unless otherwise noted, a signal may appear more than once, or not at all, in a signal list. In most cases, the end of the signal list is unambiguous (since signal numbers are never negative, and signal names rarely if ever begin with '-', an option argument beginning with '-' is a reliable indicator). In unusual cases, you may need to arrange options so that the signal list is at the end of the command, or so that it is followed by an argument that cannot be interpreted as a signal number.


Your comments on this guide, and on the software that it documents, are welcome. Please send them to:

George B. Moody (george@mit.edu)

13 March 2014

Up: WFDB Applications Guide


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Updated 13 March 2014