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<p>

Two sets of annotations are supplied with the data for the

<a href="/challenge/2000/">Computers in Cardiology Challenge

2000</a>.  These can be identified by the file name suffixes <tt>.apn</tt>

and <tt>.qrs</tt>.

<p>

The <tt>.apn</tt> files contain apnea annotations.  These are currently

available for the 35 records in the learning set only; those for the test set

will be posted here after the conclusion of the Challenge in September.  (To

view these annotations, use <a

href="/physiotools/wag/rdann-1.htm"><tt>rdann</tt></a> to convert the binary

annotation files into text.  If you have not used <tt>rdann</tt> previously,

see the detailed instructions <a href="#rdann-notes">below.</a>) These

annotations have been prepared on the basis of expert visual review of

simultaneously recorded respiration and oxygen saturation signals.  These

additional signals can be studied for 8 records (a01er - a04er, b01er, and

c01er - c03er; these contain the same ECG data as a01 - a04, b01, and c01 -

c03, respectively).

<p>

When these files were first posted here, the following (incorrect) description

of the <tt>.apn</tt> annotation files was also posted:

<blockquote>

In these files, an "A" annotation indicates that apnea occurs during the

<em>following</em> one-minute interval, and an "N" annotation indicates that

there is no apnea during the following one-minute interval.

</blockquote>

<p>

Following is a corrected description:

<blockquote>

In each of these files, the first annotation is placed at 0 seconds and is

associated with the following one-minute interval (i.e., 0-59.99 seconds

elapsed time from the beginning of the record), the second annotation is placed

at 60 seconds and is associated with the next one-minute interval (60-119.99

seconds), etc.  Each "A" annotation indicates that apnea was in progress <em>at

the beginning of the associated minute</em>; each "N" annotation indicates that

apnea was not in progress at the beginning of the associated minute.  The

diagram below may help to clarify this:

<pre>

|       |       |       |       |       |       |       |       |

        ****************              ********     ********

N       A       A       N       N       A       N       A       N

</pre>

In this diagram, elapsed time is represented by distance from the left edge.

The '*'s mark apneic periods, the '|'s mark the times of the <tt>.apn</tt>

annotations (0, 60, 120, ... seconds), and the "N"s and "A"s are the "no apnea"

and "apnea" annotations.

</blockquote>

<p>

The <tt>.qrs</tt> files were created using <a

href="/physiotools/wag/sqrs-1.htm"><tt>sqrs125</tt></a>, initially with its

default threshold (250).  In these files, all detected beats (including any

abnormal beats that were detected) are marked with "N" annotations, and

QRS-like artifacts are marked with "|" annotations.  Based on visual review of

the heart rate time series (using <a

href="/physiotools/wag/hrfft-1.htm"><tt>hrplot</tt></a>), and review of

selected portions of the original ECGs and annotations (using <a

href="/physiotools/wag/wave-1.htm">WAVE</a>), <tt>sqrs125</tt> was run again

using its <tt>-m</tt> option to select lower thresholds on some recordings (in

some cases, more than once) to obtain better detection of low-amplitude QRS

complexes.  In no case were the annotations hand-edited.  Only small numbers of

annotations were inspected in each recording to determine if the threshold had

been set appropriately.  If you wish to experiment further with

<tt>sqrs125</tt> or with your own QRS detector, it may be helpful to know

exactly how the <tt>.qrs</tt> files provided here were made, so here are the

commands that are needed to do so:

<pre>

sqrs125 -r a01

sqrs125 -r a02 -m 125

sqrs125 -r a03

sqrs125 -r a04

sqrs125 -r a05

sqrs125 -r a06 -m 125

sqrs125 -r a07

sqrs125 -r a08

sqrs125 -r a09

sqrs125 -r a10

sqrs125 -r a11

sqrs125 -r a12 -m 125

sqrs125 -r a13

sqrs125 -r a14

sqrs125 -r a15

sqrs125 -r a16

sqrs125 -r a17 -m 100

sqrs125 -r a18

sqrs125 -r a19

sqrs125 -r a20 -m 125

sqrs125 -r b01

sqrs125 -r b02 -m 125

sqrs125 -r b03 -m 125

sqrs125 -r b04 -m 75

sqrs125 -r b05 -m 125

sqrs125 -r b06

sqrs125 -r b07

sqrs125 -r b08

sqrs125 -r b09

sqrs125 -r b10

sqrs125 -r c01 -m 125

sqrs125 -r c02

sqrs125 -r c03

sqrs125 -r c04 -m 125

sqrs125 -r c05 -m 125

sqrs125 -r c06 -m 125

sqrs125 -r c07 -m 100

sqrs125 -r c08 -m 100

sqrs125 -r c09

sqrs125 -r c10

sqrs125 -r x01

sqrs125 -r x02

sqrs125 -r x03

sqrs125 -r x04

sqrs125 -r x05

sqrs125 -r x06

sqrs125 -r x07

sqrs125 -r x08

sqrs125 -r x09

sqrs125 -r x10

sqrs125 -r x11

sqrs125 -r x12

sqrs125 -r x13

sqrs125 -r x14 -m 125

sqrs125 -r x15 -m 125

sqrs125 -r x16

sqrs125 -r x17 -m 50

sqrs125 -r x18

sqrs125 -r x19

sqrs125 -r x20

sqrs125 -r x21

sqrs125 -r x22

sqrs125 -r x23

sqrs125 -r x24

sqrs125 -r x25

sqrs125 -r x26

sqrs125 -r x27

sqrs125 -r x28

sqrs125 -r x29 -m 125

sqrs125 -r x30

sqrs125 -r x31

sqrs125 -r x32

sqrs125 -r x33 -m 125

sqrs125 -r x34 -m 125

sqrs125 -r x35

</pre>

<a name="rdann-notes"><h2>How to use <tt>rdann</tt></h2></a>

<p>

<strong>Install <tt>rdann</tt>:</strong>

<p>

If you haven't already downloaded and installed <tt>rdann</tt>, do so now.

Search for <tt>rdann</tt> (type <tt>rdann</tt> into the text box above

the <em>Search</em> button in the left margin of this page, then click

on <em>Search</em>), and you will find the C-language source as well

as a UNIX-style manual page that describes <tt>rdann</tt>'s options

in more detail than below.  All versions of <tt>rdann</tt> are compiled from

the same source, so you can create a version for your operating system,

provided that you have a C compiler.  If you do this, you will also need to

download and compile the sources for the

<a href="/physiotools/wfdb.shtml">WFDB library</a> used by <tt>rdann</tt>.

<a href="/physiotools/binaries">Binaries</a> (executable versions of the

program) for several popular operating systems can also be downloaded.  Note

that <tt>rdann</tt> is a text-mode application;  users of MS-Windows can run

the MS-DOS version of <tt>rdann</tt> in a DOS window.

<p>

<strong>Locate the files you need:</strong>

<p>

Each of the data files has a <em>record name</em> (the first part of the

file name, before the '.') and a suffix (the second part of the file name,

following the '.').  For example, the file <tt>a19.apn</tt> has the record

name <tt>a19</tt> and the suffix <tt>apn</tt>.

<p>

Files with <tt>qrs</tt> or <tt>apn</tt> suffixes are binary annotation files.

For these files, the suffix is the <em>annotator name</em>.  Files with the

suffix <tt>hea</tt> are (text) header files containing information about the

format of the related files, and those with the suffix <tt>dat</tt> are binary

signal files (containing digitized samples of the ECG and other signals).

<p>

In order to read an annotation file successfully, you will need to download

both the annotation file itself and the associated header file.  For example,

to read <tt>a19.apn</tt>, download <tt>a19.apn</tt> and <tt>a19.hea</tt>.

(The Linux version of <tt>rdann</tt> can act as an HTTP client and can read the

files directly from the PhysioNet server without the need to store them

locally.  If you have compiled your own version of the WFDB library with

<a href="/physiotools/wpg/wpg_43.htm">NETFILES</a> support, your version

of <tt>rdann</tt> will also have this capability.)

<p>

<strong>Use <tt>rdann</tt> to convert binary annotations to text:</strong>

<p>

Once you know the <em>record name</em> and the <em>annotator name</em>, you can

use <tt>rdann</tt> to read the file.  For example, to read <tt>a19.apn</tt>,

use the command

<pre>

     rdann -r a19 -a apn -f 0

</pre>

<p>

This command will produce output on the screen that begins:

<pre>

    0:00.000        0     N    0    0    0

    1:00.000     6000     A    0    0    0

    2:00.000    12000     A    0    0    0

    3:00.000    18000     A    0    0    0

    4:00.000    24000     A    0    0    0

    5:00.000    30000     A    0    0    0

    6:00.000    36000     A    0    0    0

    7:00.000    42000     N    0    0    0

    8:00.000    48000     N    0    0    0

    9:00.000    54000     A    0    0    0

   10:00.000    60000     A    0    0    0

</pre>

(The '-f 0' option was not required by the version of rdann that was

available when this page was written.  If omitted, the first annotation,

at 0:00.000, will not appear in the output.)

<p>

To capture the output of <tt>rdann</tt> in a file, redirect it using a command

such as:

<pre>

     rdann -r a19 -a apn -f 0 &gt;<font color=blue><em>textfile</em></font>

</pre>

In this command, replace <font color=blue><tt><em>textfile</em></tt></font>

with any desired file name.  This method works under MS-DOS/Windows

as well as under all versions of UNIX.

<p>

Each line of <tt>rdann</tt>'s output corresponds to one annotation.  The first

two columns indicate the elapsed time (i.e., the interval) from the beginning

of the record to the sample marked by the annotation. (Column 1 gives this in

hours, minutes, and seconds, and column 2 gives the same information in sample

intervals.  In these records, one sample interval equals 10 milliseconds.)  The

third column contains a mnemonic code for the annotation type.  As noted above,

in the <tt>apn</tt> files, these codes are <tt>A</tt> for "apnea" and

<tt>N</tt> for "no apnea".  In the <tt>qrs</tt> files, the codes are <tt>N</tt>

for a QRS complex and <tt>|</tt> for a QRS-like artifact.  In these annotation

files, the remaining columns can be ignored.

<p>

The sample output shown above can therefore be interpreted thus: during the

first minute (beginning at 0:00.000, or sample number 0) there is no apnea

(<tt>N</tt>); during each of the next several one-minute periods (beginning at

1:00.000, 2:00.000, 3:00.000, ...), there is apnea (<tt>A</tt>).

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