Two sets of annotations are supplied with the data for the Computers in Cardiology Challenge 2000. These can be identified by the file name suffixes .apn and .qrs.
The .apn 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 rdann to convert the binary annotation files into text. If you have not used rdann previously, see the detailed instructions below.) 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).
When these files were first posted here, the following (incorrect) description of the .apn annotation files was also posted:
In these files, an "A" annotation indicates that apnea occurs during the following one-minute interval, and an "N" annotation indicates that there is no apnea during the following one-minute interval.
Following is a corrected description:
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 at
the beginning of the associated minute; 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:
| | | | | | | | |
**************** ******** ********
N A A N N A N A N
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 .apn
annotations (0, 60, 120, ... seconds), and the "N"s and "A"s are the "no apnea"
and "apnea" annotations.
The .qrs files were created using sqrs125, 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 hrplot), and review of selected portions of the original ECGs and annotations (using WAVE), sqrs125 was run again using its -m 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 sqrs125 or with your own QRS detector, it may be helpful to know exactly how the .qrs files provided here were made, so here are the commands that are needed to do so:
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
Install rdann:
If you haven't already downloaded and installed rdann, do so now. Search for rdann (type rdann into the text box above the Search button in the left margin of this page, then click on Search), and you will find the C-language source as well as a UNIX-style manual page that describes rdann's options in more detail than below. All versions of rdann 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 WFDB library used by rdann. Binaries (executable versions of the program) for several popular operating systems can also be downloaded. Note that rdann is a text-mode application; users of MS-Windows can run the MS-DOS version of rdann in a DOS window.
Locate the files you need:
Each of the data files has a record name (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 a19.apn has the record name a19 and the suffix apn.
Files with qrs or apn suffixes are binary annotation files. For these files, the suffix is the annotator name. Files with the suffix hea are (text) header files containing information about the format of the related files, and those with the suffix dat are binary signal files (containing digitized samples of the ECG and other signals).
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 a19.apn, download a19.apn and a19.hea. (The Linux version of rdann 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 NETFILES support, your version of rdann will also have this capability.)
Use rdann to convert binary annotations to text:
Once you know the record name and the annotator name, you can use rdann to read the file. For example, to read a19.apn, use the command
rdann -r a19 -a apn -f 0
This command will produce output on the screen that begins:
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
(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.)
To capture the output of rdann in a file, redirect it using a command such as:
rdann -r a19 -a apn -f 0 >textfile
In this command, replace textfile
with any desired file name. This method works under MS-DOS/Windows
as well as under all versions of UNIX.
Each line of rdann'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 apn files, these codes are A for "apnea" and N for "no apnea". In the qrs files, the codes are N for a QRS complex and | for a QRS-like artifact. In these annotation files, the remaining columns can be ignored.
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 (N); during each of the next several one-minute periods (beginning at 1:00.000, 2:00.000, 3:00.000, ...), there is apnea (A).