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Have you read this FAQ? If not, please take a few minutes to do so. It answers many common questions.
Have you tried searching for key words using a PhysioNet search, or a Google search? Did you notice that there is a search form at the top of almost every page on PhysioNet? If not, please try a search now by clicking on one of the many links that you will find here and there in this paragraph.
If you have not found an answer to your question in the PhysioNet FAQ or by a search, you may wish to ask your question by email. If everyone who took the time to ask a question by email first took the time to read How to Ask Questions the Smart Way, we would be able to take the time to answer all of the questions we receive with the detailed and pertinent answers they deserve. Since this will never happen, we give priority in answering questions to those who have read this FAQ. How can we tell who has done so? That's easy; we look for the magic word in the subject line of the email. (Important: the author of "How to Ask Questions the Smart Way" cannot answer your questions; read his disclaimer!)
You're looking at the PhysioNet web site, or one of its mirrors. Read more about PhysioNet and the NIH-sponsored research resource to which it belongs here.
We have large collections of physiologic signals (time series) and software that can be used to study these signals, and smaller but growing collections of research papers, tutorials, and reference materials that relate to the signals and software.
We are a diverse group of computer scientists, physicists, mathematicians, biomedical researchers, clinicians, and educators at MIT (Cambridge, MA, USA), the Beth Israel Deaconess Medical Center/Harvard Medical School (Boston, MA, USA), Boston University (Boston, MA, USA), and McGill University (Montréal, QC, Canada). Many of us have worked together for 20 years or even longer on problems relating to characterizing and understanding the dynamics of human physiology and the implications of dynamical change in diagnosis and treatment of pathophysiology.
PhysioNet receives contributions of data, software, publications, and tutorials from researchers worldwide; see the PhysioNet Contributors page for a list.
You can't learn everything there is to know about snow by studying a single snowflake, or even a few hundred of them. In much the same way (and for some of the same reasons), physiologic signals display astonishing diversity, between individuals and even within individual subjects over time. To study them seriously requires large amounts of data that are difficult and expensive to gather and to characterize, and software that can be flexibly and efficiently modified to meet the unique requirements of new research.
PhysioNet is here first of all because we (see the previous question) needed to gather such data and to design such software for our own work. Having done so, we believe that other researchers should not be forced to do the same, and that by making our data and software available, others should be able to explore them, to develop, test, and refine hypotheses; in short, to do investigations that would not be possible otherwise.
Many researchers around the world share this vision of open science, in which investigators who need data with which to test their ideas can bootstrap their studies using large, freely available, and well-understood data collections, and in which investigators wishing to explore their data using a wide variety of methods can find verifiable, open-source, reference implementations of analysis software that can be adapted to their own studies. PhysioNet began in 1999 with our own collections of data and software, but its archives continue to grow in scope and depth thanks to the contributions of many others.
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Who can use data and software from PhysioNet?
These materials have placed here for the use of researchers anywhere in the world (our visitors in the month of January, 2000 came from over 50 countries on every continent except Antarctica). Many of them are biomedical researchers in academia and industry, but others include physicists, mathematicians, computer scientists, educators, graduate and undergraduate university students, and even secondary school students.
Update: PhysioNet visitors came from at least 90 countries during the month of May, 2003. If you're reading this in Antarctica, please let us know!
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Is all of this really free?
Yes.
We encourage contributions of data and software to PhysioNet, but only if contributors are willing to allow their contributions to be used freely. See our guidelines for contributors and our copying policy.
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How can I buy a copy of ...?
See the answer to the previous question.
Printed copies of some of our books are now available at the PhysioNet Bookstore.
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Please send me a copy of ...
Everything we have is free, and can be freely redistributed. You can download it yourself, or you can ask a friend to download it for you. We understand that web access can be slow or expensive in some locations; please understand that preparing and mailing materials from this web site to individual users would also be slow and expensive.
For downloading tips, read the questions and answers below, beginning with How can I download binary files?.
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What are the license terms?
The software is licensed under the GNU Public License (GPL), or (if noted in the source files) other licenses that conform to the Open Source Definition. These licenses permit verbatim copying and redistribution of the source files, and generally grant other permissions as well. For further details, see Can I use your code in my commercial application? (below).
There is nothing analogous to the GPL for data, but we permit copying and redistribution of unaltered data from this site without restrictions, in the spirit of the GPL. We do not allow distribution of altered data except under conditions that make it clear that the data have been altered, because it is very important that users should be able to distinguish between original data from this site and modified versions of those data.
Other materials from this site (books, tutorials, papers, and commentary) may be reproduced freely, with appropriate credit to the original authors.
See the PhysioNet Copying Policy for further details.
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Is this software Y2K-compliant?
Yes. See our statement of Y10K compliance.
This really isn't a frequently-asked question any more. The last person who asked it sent his question by email, dated 1 January 103.
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My connection is slow. Is there a mirror?
Yes. See Mirrors for a list.
Yes. Please use rsync as described in How to set up a mirror of PhysioNet.
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Where can I find data for healthy subjects?
Most data in PhysioBank have been obtained from subjects with a variety of health problems. Several PhysioBank databases, however, include healthy subjects.
The control records (c01, c02, ... c10) from the Apnea-ECG Database were obtained from healthy volunteers during sleep; the recordings each contain a single ECG signal and are each about 8 hours long. Simultaneously recorded respiration and oxygen saturation signals are available for one of these recordings.
The Fantasia Database is a very well-controlled set of 2-hour recordings of ECG (with beat annotations) and respiration signals from 40 rigorously-screened healthy subjects (20 young, 20 elderly, with equal numbers of men and women in each group). Half of the recordings also include an uncalibrated continuous non-invasive blood pressure signal.
Heart rate time series from five additional groups of healthy volunteers are available in a collection of data used for a study of exaggerated heart rate oscillations during meditation (two groups of meditators recorded before and during meditation, a group of volunteers recorded during sleep, a group of volunteers recorded during metronomic (fixed-rate) breathing, and a group of elite athletes recorded during sleeping hours).
The PTB Diagnostic ECG Database includes records from 54 healthy volunteers; here is a list of them.
The MIT-BIH Normal Sinus Rhythm Database consists of ECG recordings from subjects who were found to have had no significant arrhythmias, ST changes, or known cardiac disease. Since these subjects were recorded for medical reasons, however, they are not necessarily "healthy" -- but their medical problems are not heart-related. Subjects included in the Normal Sinus Rhythm RR Interval Database were known to be healthy, however.
The Sleep-EDF Database contains EEG, EOG, and other signals from 8 healthy subjects. (Four of these had mild difficulty falling asleep, but were otherwise healthy.)
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Is the AHA Database available on PhysioNet?
No, it is currently available only from ECRI. Additional information about the AHA Database is available here.
A single sample record that was prepared as an example by the creators of the AHA Database is available in PhysioBank.
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Are there any 12-lead (diagnostic) ECGs in PhysioBank?
The PTB Diagnostic ECG Database contains 549 twelve-lead ECGs from 294 subjects.
The NHLBI maintains a registry of diagnostic ECG databases. The CSE Database and the 12-lead ECG Library may also be of interest.
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Are updates for CD-ROM databases of physiologic signals available here?
Yes. Find them here.
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How can I download binary files?
The details of doing this depend on your web browser, not on anything specific to PhysioNet or to the specific files you wish to download, so the first thing you should do is to learn how to use your web browser. Most browsers have a Help button that can get you started.
Many web browsers, including Galeon, Konqueror, Mozilla, Netscape, and Opera, but not including Firefox, Lynx, MS Internet Explorer, or Safari, allow you to download a file by pressing and holding the Shift key while left-clicking on the link to the file you wish to download.
In Firefox, right-click on the link, and choose "Save Link As..." from the popup menu.
In Lynx, press d to download the target of the highlighted link.
If you are using MS Internet Explorer, it is often possible to download a file simply by left-clicking on the link to that file. This is not a foolproof method, however, since MSIE attempts to guess the file type and may attempt to open the file rather than downloading it. A more reliable method is to right-click on the link and then to choose Save Target As... from the pop-up menu that appears. In most cases, you can accept the suggested file name, but be aware that MSIE will generate a .txt extension for any file that has a name without an extension (such as the files named Makefile that are found throughout PhysioToolkit), so you will need to correct these file names.
In Safari, right-click (or, with a single-button mouse, press the Control key and click), and choose "Download Linked File".
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Can I download an entire PhysioBank database in one step?
Yes. Before you do so, however, note that this may not be necessary.
The recommended way to read PhysioBank data files is by using either PhysioToolkit software linked to the WFDB library, or (for those who like to write their own code) your own software linked to the WFDB library. In either case, the WFDB library does the work of finding and reading PhysioBank files. If you have a local copy of a PhysioBank file, the WFDB library reads that copy; otherwise, it reads the file from PhysioNet using the same HTTP protocol that your web browser uses.
If you want to read PhysioBank files without using the WFDB library (but why?) you will probably need to reformat the files into some less storage-efficient format first, and to do that you will need to read the original files using the WFDB library. In that case, you may as well allow the WFDB library to read the original files via HTTP, and write only the reformatted files to local storage.
If (despite all of the above) you decide to download a local copy of an entire database, there are two ways to do so that are much more efficient than downloading the files one at a time using a web browser.
The first method uses rsync, which is the same free software used by the PhysioNet mirrors. Install rsync if you don't have it already, and then use the command
rsync physionet.org::
to get a list of databases available via rsync. The output
of this command will contain lines such as
aami-ec13 ANSI/AAMI EC13 Test Waveforms (1 Mb)
afdb MIT-BIH Atrial Fibrillation Database (607 Mb)
afpdb PAF Prediction Challenge Database (195 Mb)
aftdb AF Termination Challenge Database (3 Mb)
The entries in the first column are names of available "modules" (sets of
files). To download (for example) the AF Termination Challenge Database
into a subdirectory of its own within /usr/database, type:
rsync -Cavz physionet.org::aftdb /usr/database/aftdb
(You may, of course, use any directory for storage of the downloaded files. The suggested directory, /usr/database, is searched by default by the WFDB library, so it's a good choice.)
Using rsync is particularly convenient if you have an unreliable connection; if the transfer is interrupted, simply repeat the command once the connection has been re-established, and rsync will quickly determine where it needs to resume the download. Another advantage of using rsync is that it preserves the timestamps of the original files on PhysioNet, so that if you return to PhysioNet, it will be easy to see if the original files have been updated since the last time you downloaded them. Note that rsync has its own IANA-assigned port (873); if you can reach PhysioNet with your web browser (port 80, HTTP) but not via rsync, your firewall may be blocking port 873.
The second method is described in the answer to the next question. Choose it if you can't use rsync, or if your connection to one of the PhysioNet mirrors (which do not generally support rsync access) is much better than your connection to the PhysioNet master server.
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There are so many files in .... Can I get a zip file or a tar archive of
it?
You can try looking for a .zip or a .tar.gz archive in the directory that contains the files of interest, or in its parent directory. If you don't find one, however, the answer is no. It is necessary to keep individual files available, and maintaining redundant copies of these files within archives, or creating them on demand, would not be the best use of available resources.
There are excellent alternatives, however, to downloading many files one at a time using a web browser. Try using a utility that can do batch-oriented HTTP transfers, such as wget, available from this site in source form for Unix, Mac OS/X, or MS-Windows, or in binary form for MS-Windows. Once you have installed wget, retrieve a batch of files using a command such as
wget -r -np http://physionet.org/physiobank/database/mitdb/
(or substitute the name of a nearby
PhysioNet mirror for
physionet.org above).
If you would like to download an entire PhysioBank database, see the previous question.
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How can I unpack a .tar.gz archive?
These are gzip-compressed tar archives. If you have the GNU tar utility (included in all GNU/Linux distributions and many other versions of Unix including Mac OS X (Darwin), and available for MS-Windows as part of the free Cygwin software development package), you can unpack foo.tar.gz in one step:
tar xfvz foo.tar.gzIf you have another version of tar, it may not support the z option, and you may need to decompress using gzip before unpacking, like this:
gzip -d foo.tar.gz(If you don't have gzip, free versions are available for all popular operating systems from gzip.org.)
tar xfv foo.tar
If your browser decompressed the archive while downloading it, simply unpack it:
tar xfv foo.tar
The popular WinZip utility can unpack .tar and .tar.gz archives under MS Windows, but it does not recognize .tar.gz format unless the file names end in .tar.gz (as such files appear on this site). Your browser may rename such files when you download them, replacing the first ``.'' with ``_''. Before attempting to unpack them with WinZip, restore their original names. Thanks to Paul Knopp for this tip!
By convention, each of the .tar.gz archives on PhysioNet has been constructed so that it unpacks into a subdirectory (created by tar if necessary) within the current directory. An archive named foo.tar.gz would normally be unpacked into a subdirectory named foo. Look at the file names printed by tar during the unpacking process to see where the unpacked files have been written.
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Can I get these files via FTP?
No. It is considered insecure for an FTP server and a web server to share a file system, and it is not practical for us to maintain separate web and FTP servers.
If you are interested in batch file transfers, read the answer to "There are so many files in ....", above.
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Can I look at the waveforms using only my web browser?
Yes. Choose a recording first (look in the PhysioBank Archives to find one), then go to the Chart-O-Matic and fill in the form. For a sample, click here.
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What are .dat, .hea, .atr, .qrs, ... files?
Files belonging to PhysioBank databases have two-part names: the first part is the record name, and the second part (following the ".") indicates the file type. For example, a file named "chf08.hea" is a file of type .hea (see below) belonging to a record named "chf08".
All of these file types are found in PhysioBank databases:
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What are .xws files and how can I view them?
These are short text files that point to specific locations within the records with which they are associated. You can view the same locations using, for example, the Chart-O-Matic. If you haven't set up a browser helper application for viewing .xws files, you can read them as text and copy the record, annotator, and starting time data into the Chart-O-Matic form.
You can set up WAVE (actually, wavescript) as a helper application for your browser so that when you click on a .xws file, WAVE will open the associated record at the specified location using its builtin HTTP client code (this is much faster and more flexible than using the Chart-O-Matic). See Controlling WAVE from a web browser in the WAVE User's Guide for details.
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What is a ``record name'' or an ``annotator name''?
Records are identified by record names, which contain letters, digits, and underscores. For example, the MIT-BIH Arrhythmia Database has record names consisting of three-digit numbers beginning with `1' or `2', and the European ST-T Database has record names that are four-digit numbers prefixed by `e'. Case is significant in record names that contain letters, even in environments such as MS-DOS 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. A record is comprised of several files, which contain signals, annotations, and specifications of signal attributes; each file belonging to a given record normally includes the record name as part of its name. The files named RECORDS found in the PhysioBank database directories list the record names for each database.
There may be many annotation files associated with the same record; they are distinguished by annotator names. The name of an annotation file is the record name, followed by a `.', followed by the annotator name. The files named ANNOTATORS found in the PhysioBank database directories list the annotator names for the annotation files that are available here. The annotator name `atr' is reserved to identify reference annotation files supplied by the developers of the databases to document correct beat labels. You may use other annotator names (which may contain letters, digits and underscores, as for record names) to identify annotation files that you create. You may wish to adopt the convention that the annotator name is the name of the file's creator (a program or a person).
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How can I run ... on all of the records in a PhysioBank database?
Write a shell script to iterate over the records. You can use the (text) file called RECORDS in each database directory (see the previous question) as the list of records to be processed; wfdbcat can be used to get this file from PhysioBank. For example:
for R in `wfdbcat mitdb/RECORDS`
do
echo -n "Record mitdb/$R ..."
sigamp -r mitdb/$R -a atr -p
done
The example above runs sigamp on each record in the MIT-BIH Arrythmia Database (mitdb). Use whatever scripting language you wish; the example is written in the standard POSIX sh scripting language and can be run in a terminal window on GNU/Linux, Mac OS X, or any other UNIX, or in a Cygwin window under MS-Windows. For a tutorial introduction to writing shell scripts, try the three-part Bash by Example series or the shorter How to write a shell script [external links open in another window].
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Where are the annotation, signal, or header files I just created?
WFDB applications can read from local files or directly from remote locations such as the PhysioNet web site, but they always write to local files. In order to read annotation, signal, or header files that you have written, it will usually be simplest to begin within the directory (folder) that was current when they were created.
If you use WFDB applications to create new annotation, signal, or header files, those files are created within the current working directory (or, in some cases, its subdirectories). Thus, for example, the output annotation file created by the command
wqrs -r 100sis a file in the current directory named 100s.wqrs. If the record name contains additional path information, the output file is written in a location accessible by following that path from the current directory. For example, the command
wqrs -r mitdb/100writes its output annotation file (100.wqrs) in the mitdb subdirectory of the current working directory. If mitdb doesn't exist in the current directory, wqrs creates it.
Applications that use the WFDB library behave this way so that their output files can be located by other WFDB applications. For example, given the above, the command
wave -r mitdb/100 -a wqrsdisplays the annotations from the local file created by wqrs together with the corresponding signals from PhysioBank. Neither wqrs nor wave need to read local copies of the header or the (much larger) signal files, however. If no local copies exist, they are read directly from the PhysioNet server, using the additional path information in the record name (mitdb/, in this example) to find them.
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How were the signals in PhysioBank digitized?
They come from many sources, but in all cases the signals have been digitally recorded or digitized from analog recordings. See the descriptions of the individual databases for details.
We are occasionally asked about digitizing paper ECGs and other hard-copy data. A brief survey of this subject is available here.
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Should I use PhysioBank formats for my project?
Perhaps we're biased, but we think so, and here's why:
If you can read an entire EDF frame (often a minute of digitized signals) into memory, and if a latency on the order of the frame length is tolerable, then EDF is a good choice, also.
Some PhysioBank formats that are good choices for new projects are format 16 (very easy to read using almost any software, though not as storage efficent as format 212 if you have 12-bit or lower resolution) and format 212 (most used in PhysioBank, because it's ideal for widely available 12-bit resolution data, and it's still relatively easy to read). Format 8 is not recommended for new projects, because it does not preserve the DC offset when used in random-access mode, and because it limits the maximum slew rate of the signals that can be recorded. (It is supported for historical reasons, and it was devised as a way to circumvent memory and storage limits encountered in recording the MIT-BIH Arrhythmia Database.)
If you need even more storage efficiency than is provided by PhysioBank formats, consider using gzip or bzip2 to compress files stored in format 16 or 212, or (especially for a commercial product) consider SCP ECG.
If you need an easy-to-read format, and efficiency is not a concern, use rdsamp's output (text) format (see this note).
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How can I find out what signals were recorded?
If you are looking for recordings with a specific type of signal, look first in the PhysioBank Archive Index, which indicates in general terms the types of signals in each of the available databases.
Within each database, there may be variations in the choice of signals from record to record. The pages that describe each database (see the links from the PhysioBank Archive Index) can help in locating subsets of records that contain specific signals of interest.
Each recording has an associated header file that lists (among other things) the names of the signals included in that recording. The wfdbdesc utility reads header files and produces a readable summary of their contents, including the signal names. Many other PhysioToolkit applications that read PhysioBank data are capable of printing or displaying signal names. The Chart-O-Matic and the rdsamp-O-Matic include the signal names in output they generate for viewing on-line via a web browser.
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What do the signal names MLII, V2, ... mean?
Short answer: MLII and V2 are ECG signals. The names refer to the electrode positions, using standard nomenclature for lead names. MLII is "modified lead II", a bipolar lead parallel to the standard limb lead II, but acquired using electrodes placed on the torso (a requirement for long-term ECG monitoring). V2 is a precordial lead that is roughly orthogonal to MLII. These two leads are favored for many recordings, since MLII yields high-amplitude normal QRS complexes in most subjects, and V2 usually offers a nearly optimal frontal-plane projection of any ectopic beats that happen to be of low amplitude in MLII.
Long answer: Signals in PhysioBank databases have standardized names (see the previous question). Most of these are in common clinical use for designating signals such as arterial blood pressure (ABP), respiration (RESP), or heart rate (HR). Generally the pages that describe the databases in which these signals appear include definitions of any unusual signal names (see the links to these pages from the PhysioBank Archive Index).
Most ECG recordings contain two or more simultaneously recorded ECG signals, called "leads." Since the heart generates an electrical field that varies spatially as well as temporally, there is no uniquely determined (scalar) signal that offers a complete view of cardiac electrical activity. The standard practice among clinicians and researchers interested in the ECG is to record two or more signals (leads) derived using sensing electrodes placed at certain specific locations. Some leads are bipolar (they are potential differences between pairs of electrodes); others are unipolar (they are potentials measured with respect to an artificial "zero" reference potential typically derived by summing potentials measured at multiple locations). Confusingly, the wires that connect the electrodes to the recording equipment are also called "leads"; thus, for example, a five-lead (five-wire) harness is generally used to record a two-lead (two-signal) ECG!
The three Einthoven bipolar limb leads (designated I, II, and III) are determined by the pairwise potential differences between electrodes placed on the left arm (LA), right arm (RA), and left leg (LL); specifically, lead II is the potential difference between LL and RA. In most subjects, the axis defined by these points is roughly parallel to the mean cardiac electrical axis, so it is a lead in which QRS complexes are typically observable at nearly maximum amplitude.
In long-term ECG recordings (including most of those on PhysioNet), limb leads are not generally used, since physical activity causes significant interference in these leads. Commonly, equivalent "modified" leads are used, with electrodes placed on the torso in positions chosen so that the signals closely match the limb leads. This is possible because the cardiac electrical field is (to a good approximation) a time-varying dipole field, so that it is generally sufficient to choose positions that allow one to observe the same projections of the dipole field onto the axes defined by the limb leads.
For MLII (modified lead II), the LL equivalent electrode is ideally placed at the left iliac crest, and the RA equivalent electrode is ideally placed in the infraclavicular fossa, medial to the border of the deltoid muscle and 2 cm below the lower border of the clavicle.
Additional information about ECG lead systems can be found in many textbooks about electrocardiography. A clear and comprehensive discussion can be found in chapter 15 of Bioelectromagnetism: Principles and Applications of Bioelectric and Biomagnetic Fields by J Malivuo and R Plonsey (Oxford University Press, 1995; also available on-line here).
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What do the signal names 'signal 0', 'signal 1', ... mean?
As noted in the answers to the previous two questions, signal names recorded in header files describe the signals in each record. In rare cases, however, this information is missing, usually because it was not preserved when the signals were recorded. Names of the form 'signal N' are default signal names used in such cases; they may appear in header files explicitly, or they may be displayed by PhysioToolkit software if no explicit signal names appear in a header file.
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What is the format of the signal files?
Many formats are supported. Most signal files are written in "format 212", in which two 12-bit samples are bit-packed into three 8-bit bytes. See signal(5) in the WFDB Applications Guide for details on format 212 and on the other supported formats.
To determine which format is used for a given signal file, look in the associated header file. (This is a text file that usually has the same name as the signal file, except for a suffix of .hea instead of .dat.) Each line of the header file that begins with the name of the signal file describes the format and contents of a signal within the signal file. See header(5) in the WFDB Applications Guide for details.
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How can I read signal files?
If you would like to read signal files within a C, C++, Fortran, Java, Perl, or Python program, see the WFDB Programmer's Guide for information on doing this using the WFDB library. Other programming languages supported by SWIG may also be usable with the WFDB library, but have not been tested. Briefly, use isigopen() to open the files, and getvec() to read them.
If you would like to do this within a Matlab or Octave program, see Reading and writing PhysioBank and compatible data on the Contributed software for Matlab and Octave page. Several solutions, with varying degrees of complexity, are offered. Note that Matlab is not able to import signal files directly.
Another possibility is to convert the portions of interest into text format using rdsamp (described in detail in How to obtain PhysioBank data in text form). To save rdsamp's output in a file, or to read rdsamp's output using another program, see this note. Alternatively, segments up to a minute in length of signal files found on this web server can be converted into text using the rdsamp-O-Matic, which can be accessed using your web browser. This may be useful if you wish to read signals using Excel or another spreadsheet (although spreadsheets in general are not recommended as tools for signal processing, visualization, or analysis; there are much better choices freely available in PhysioToolkit).
MS-Windows Media Player and similar software for reading audio and multimedia files cannot be used to read these files (or any others in PhysioBank).
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You can't in general, because Matlab doesn't know how to figure out which of
the many supported formats is used in any given signal file, because it can't
understand the most commonly used formats in any case, and because (in many
cases) signal files are orders of magnitude larger than any matrix that Matlab
can handle. See How can I read signal files? for a
variety of ways to read signal files from Matlab without using its import
feature.
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You can't, because Excel doesn't know how to figure out which of the many
supported formats is used in any given signal file, because it can't understand
any of those formats in any case, and because signal files are almost always
orders of magnitude larger than any spreadsheet that Excel can handle.
Spreadsheets are not suitable for studying, visualizing, or analyzing digitized
signals; many better tools are freely available in
PhysioToolkit.
If, despite the above, you still wish to read a piece of a signal file into
a spreadsheet, see How can I read signal files?.
It's part of the free, open source
WFDB Software Package. Both C sources
and binaries for several popular operating systems are available.
Install it, then type
for a brief summary of options. For details, see
rdsamp(1) in the
WFDB Applications Guide.
The output of rdsamp is in text format. Unless you have used the
-v option, the output contains data only (no column labels) and can be
plotted directly using, for example,
plt. The first column contains
sample numbers (or elapsed times in seconds and milliseconds if you have used
the -p option), and each of the remaining columns contains samples
for one signal (in raw ADC units unless you have used the -p option).
To save rdsamp's output in a file, or to read rdsamp's output
using another program, see this note.
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Analog-to-digital converters (ADCs) are usually used to produce PhysioBank
signal files, which consist of sequences of integer samples in unscaled
analog-to-digital converter units (adus). Samples are stored in this
way not only because doing so usually requires less space than most
alternatives, but also because this scheme introduces no loss of precision
beyond the quantization error of the ADC. By default, rdsamp outputs
sample values in unscaled adus (raw ADC units).
The header file for each record
contains fields that describe the characteristics of each signal and of the ADC
used to digitize it. These fields include the signal type (such as ECG, ABP,
or SpO2), the physical units of the original analog signal (such as mV, mmHg,
or degreesC), the gain (the number of adus per physical unit), the
baseline (the sample value that would correspond to a physical value
of zero, which is often but not always at the center of the ADC range, and may
even lie outside of the ADC range), the adczero (the sample value at
the center of the ADC range, which is 0 for a bipolar ADC and a non-zero value
for an offset binary ADC), and the number of bits of ADC precision (most often
12 for PhysioBank recordings). Taken together, the values specified for these
parameters allow identification of the signals, conversion of sample values
from raw ADC units to baseline-corrected physical units and back again, and
calculation of the ADC range in raw or physical units.
Using rdsamp's -p (physical unit output) option, or using the
rdsamp-O-Matic, the sample values are presented
in baseline-corrected physical units. The signal types and units used appear
in the first two lines of rdsamp-O-Matic output; these can be viewed using
rdsamp's -v (verbose output) option. Note that in these
cases, the sample values are given to exactly three decimal places regardless
of the precision of the integer samples.
Top
This message can be produced by any application linked to the WFDB library,
including rdsamp and rdann. In order to read data files,
these applications need to find a header (.hea) file for the input
record you specify. The message indicates that the header file was not found
in any of the expected places, or that it was unreadable. There are three
common reasons why this can happen:
Top
Yes. Go to the rdsamp-O-Matic page
and request the data of interest. You can choose to view and save the
results in your browser, or you can have them sent to your e-mail address.
Top
The rdsamp-O-Matic is intended to offer
short samples of data in text form without the need for anything more
than a web browser. It is not intended to be a method for obtaining
large amounts of data. If you need more than a minute, we strongly
recommend using any of the other methods for
reading signal files described above, which do not impose any
limit on the amount of data that can be obtained. If you install the
WFDB Software Package and run
rdsamp on your own computer, for example, you can convert entire
records to text if you wish.
The rdsamp-O-Matic limits you to one minute at a time, because
signal files converted to text can be very large, and reading them
would not be possible with standard web browsers. If you do not wish
to use any of the alternatives, you may concatenate successive minutes
obtained by multiple requests to the rdsamp-O-Matic; this will allow
you to obtain the data you wish without significantly affecting other
PhysioNet users or crashing your web browser.
Top
There are many ways to create a PhysioBank-compatible record. Here is an easy
way to do so:
Records that belong to PhysioBank never have names that include upper-case
characters, so you may wish to follow the example above and include at least
one upper-case character in the names of any records you create, to avoid
any possibility of confusing them with PhysioBank records.
There are shortcuts that may be useful if your data happen to be in a format
for which a converter is available:
If you wish to annotate your record, see How
can I annotate a record?
Informally, an annotation is a note about some feature of a signal. On
this web site, an annotation is a tag (label) that "points"
to a specific sample of a digitized recording.
Most PhysioBank databases include annotations for each record. In some
cases, these may be reference annotations that have been independently
reviewed by one or more (usually, two) human experts; in others, they may be
machine annotations generated by automated signal-processing and
analysis software. The documentation for each database indicates what types of
annotations are available.
Usually, annotations mark events that are localized in time (such as
individual heart beats); sometimes, they are used to indicate persistent
attributes (such as the beginning of a period of sleep). In recordings that
contain two or more simultaneously recorded signals, an annotation can
"point" to all signals at once, or to a specific signal.
Each annotation can be thought of as an object having six attributes: the
time (the number of sample intervals that precede the sample that the
annotation marks); an annotation type (anntyp [sic], usually displayed
as a mnemonic annotation code; see the next question); three numeric
attributes (subtyp [sic], chan, and num); and an
optional string (the aux string). Only the time attribute
has a fixed meaning; all of the others can be redefined to fit the
characteristics of the data and the needs of the investigator.
Annotations are kept in files that exist independently of the signals that
they annotate; this means, among other things, that multiple sets of
annotations (created by different applications or people) can coexist, and that
annotations can be read even if the signals to which they refer are not
available.
Within an annotation file, annotations are stored in a compact binary
format. See the questions and answers below for information about reading
annotation files.
Top
Programs such as the Chart-O-Matic and the rdann-O-Matic display annotations using these and
other codes. When these codes are used to annotate ECGs, N is a
normal sinus beat, V is a ventricular ectopic beat, S is a
supraventricular ectopic beat, and F is a fusion of a normal beat and
a ventricular ectopic beat. These and many others are described here.
Top
Most annotations occupy two bytes, of which 10 bits contain the interval
(in sample intervals) from the previous annotation, and 6 contain an annotation
type code. Special type codes allow for annotations at intervals that exceed
1023 sample intervals, and for other numeric and text fields to be associated
with individual annotations. See
annot(5) in the
WFDB Applications Guide for details.
Top
If you would like to read annotation files within a C, C++, Fortran, Java,
Perl, or Python program, see the WFDB Programmer's
Guide. Other programming languages supported by SWIG may also be usable with the
WFDB library, but have not been tested. Briefly, use annopen() to
open the files, and getann() to read annotations from them.
If you would like to do this within a Matlab or Octave program, see Reading and writing PhysioBank and
compatible data on the Contributed
software for Matlab and Octave page. Several solutions, with
varying degrees of complexity, are offered.
Another possibility is to convert the portions of interest into text format
using rdann
(described in detail in How
to obtain PhysioBank data in text form). rdann can be
downloaded as part of the WFDB Software
Package and run on your own computer. To save rdann's output in a
file, or to read rdann's output using another program, see this note. Alternatively, annotation files found on this web
server can be converted into text using the
rdann-O-Matic, which can be accessed using your web
browser. The format of rdann's text output is described below.
Top
This message can be produced by any application linked to the WFDB
library that attempts to read annotation files. In order to do so
successfully, these applications need to find the annotation file for the
annotator and input record you specify. The message indicates that the
annotation file was not found in any of the expected places, or that it was
unreadable. There are several common reasons why this can happen:
It's part of the free, open source
WFDB Software Package. Both C sources
and binaries for several popular operating systems are available.
Install it, then type
for a brief summary of options. For details, see
rdann(1) in the
WFDB Applications Guide.
The format of rdann's output is described in the answer to the
next question.
To save rdann's output in a file, or to read rdann's output
using another program, see this note.
Top
The output contains one annotation per line; from left to right, each line
contains the time of the annotation in hours, minutes, seconds, and
milliseconds; the time of the annotation in sample intervals; a mnemonic for
the annotation type; the annotation subtyp [sic], chan, and
num fields; and the auxiliary information string, if any. The
meanings of the annotation type mnemonics and of the other fields are discussed
here.
For example, if we read the first five seconds of the reference (atr)
annotations for record 200 of the MIT-BIH Arrhythmia Database using the
command
In some cases, the times in the first column may be enclosed in square brackets
[like this]. This format indicates that the times are given as times of
day (in the local time zone where the recording was made). Bracketed times may
also include the date (in DD/MM/YYYY format), if this information is available.
If the time of the beginning of the recording is not available, the times in
the first column are not bracketed, and in this case they represent the elapsed
time from the beginning of the recording.
Top
Yes. Go to the rdann-O-Matic page
and request the data of interest. You can choose to view and save the
results in your browser, or you can have them sent to your e-mail address.
Top
If the signals you wish to annotate are not already in a PhysioBank-compatible
format, including .dat and .hea files, follow the
instructions in How can I create a
PhysioBank-compatible record from my own data?
If your record contains ECG or blood pressure signals, you may wish to make a
beat annotation file. There are several
ways to create one using PhysioToolkit software:
You should always review the beat annotation file generated by any of these
detectors; although all of them work well in most cases, there is wide
variability among recordings, and any detector will make errors if the data
quality is insufficient. There are, once again, several ways to do this:
All four of these detectors mark all detected beats as normal (N). If your
record includes abnormal beats, change the N annotations for these beats to the
correct annotations (a complete list of annotation types can be found here). This can be done manually
using WAVE.
Another possibility is to use OSAS, free software for QRS detection and beat
classification available from its author (follow the link for details). This
may be particularly helpful if your records contain more than a handful of
abnormal beats, since OSAS can find most abnormal beats and annotate them
appropriately, but it is still necessary to review the automatically-generated
annotation file and correct any errors.
If you have annotations (or their equivalent) that must be converted into
PhysioBank-compatible annotation file format, it may be easiest to convert
them first into a text format that can be read by rr2ann, which can then
be used to produce the desired (binary) annotation file. If you wish to
use any of the optional annotation attributes (subtyp, chan,
num, or aux),
rr2ann will not be sufficient. In this case, you may wish
to convert your data first into rdann's output
(text) format; this can be read as input by wrann,
which will convert the data into PhysioBank-compatible annotation format.
If you do this, note that the first column (time in hours, minute, and
seconds) must be present but need not be valid, since wrann determines
the annotation times from the second column (time in sample intervals); note
also that entries in the last column may be omitted for any annotations
that have an empty aux field. Both rr2ann and wrann
read text-format data from their standard input.
Top
Don't do this!
With few exceptions, PhysioToolkit applications run in text mode
(i.e., they do not include a graphical user interface). These programs are
intended to be run within a terminal emulator using a command-line interface.
In most cases, if you attempt to run them by clicking on their icons or names,
or by entering the program name in the MS-Windows Run... dialog box,
these programs will open a DOS box, print a usage summary, and exit, usually
much too fast for you to read anything.
By far the best way to use these programs under MS-Windows is to install a
Unix-compatible terminal emulator and shell in which to run them. The best of
these is also free; if you have not already done so, download and install the
Cygwin software package.
This package includes bash (the GNU Bourne Again Shell), and a
terminal emulator in which to run it. After a standard installation of Cygwin,
you can launch a terminal emulator and bash by clicking on the Cygwin
icon that will have been installed on your desktop.
If you do not wish to use Cygwin, it is possible to run text-mode
applications under MS-Windows within a DOS box, but there are many limitations
of command.com that may prove frustrating. In particular,
command.com supports a relatively small space for environment
variables that is not secure against buffer overruns, and has idiosyncratic
filename globbing behavior.
Top
These concepts are common to all text mode applications (see the previous
question). A program's standard input is whatever it reads from the
keyboard (i.e., whatever you type into its terminal emulator window once the
program begins to run). A program's standard output is whatever it
prints in its terminal emulator window. There are (of course) exceptions,
and the exceptions are what make these ideas useful!
First, it's possible to redirect either or both of the standard
input and the standard output before the program begins to run, by adding
appropriate parameters to the command line. So, for example, a program
named pour can read its standard input from a file named
teapot, and then write its standard output to another file named
teacup, using a command such as:
Second, most applications have an additional standard error
output that is also printed in the terminal window, intermingled with
the standard output. The standard error output is reserved for warning and
error messages. If you redirect the standard output to a file, the standard
error output still appears in the terminal window (and is not copied into
the file). In most cases, this is useful behavior, since it allows you to
see quickly if there have been any errors or warnings without the need to
look through what may be lengthy output. If you wish, you can capture the
standard error output in its own file using a command such as:
Top
If you are running programs from a command prompt (by typing commands
into a terminal emulator window or an MS-DOS box), these things can
be done easily.
If you have ever used GNU/Linux, Unix, or MS-DOS, you may have captured the
output of a program by redirecting it to a file, like this:
There is an analogous operator that arranges for a program's standard input
(which would normally be read from whatever you type on the keyboard) to
be read from a file instead:
You can combine input and output redirection in a single command using the
pipe (|) operator:
You can use these techniques whenever you run programs from a command
prompt, whether those programs are among those available here or obtained
from some other source. You can use the same techniques with programs
you write yourself; the only requirement is that your programs must read from
the standard input and write to the standard output (i.e., they must not
attempt to bypass the standard input/output mechanism by reading directly from
the keyboard or writing directly to the screen).
These operators (>, >>, <, and
|) are supported by all shells (command interpreters)
under Unix, GNU/Linux, Mac OS X, and MS-DOS (including those that run within
MS-DOS boxes or other types of terminal emulators under MS-Windows). For
further information, please refer to the documentation for your shell or
command interpreter.
Top
Top
These files are included with the WFDB library. Most of the PhysioToolkit
applications use at least one of them; if you are trying to compile such an
application, you will need to have installed the WFDB library and its *.h files
first. The easiest way to do this is to install the WFDB Software Package,
which includes the WFDB library and many of the PhysioToolkit applications.
Find instructions for doing so in the quick start guide for your platform (FreeBSD, GNU/Linux, Mac OS X (Darwin), MS-Windows, and Solaris), or on the
WFDB Software Package introductory
page.
If you have already installed the WFDB Software Package and your
compiler is still complaining, the WFDB *.h files may not be installed in
any of the directories where your compiler is looking for them. Use
wfdb-config to find out where
they are.
Top
These are among the functions defined in the WFDB library; most of the
PhysioToolkit applications use at least one of these functions. If you
are trying to compile such an application, it must be linked to the
WFDB library. If you have not yet installed the WFDB library, see the
answer to the previous question.
For details on how to link to the WFDB library,
see Compiling a Program with the
WFDB Library in the WFDB Programmer's
Guide.
Top
If you are using one of the precompiled versions of the library, be sure
that you have the correct version for use with your compiler and operating
system. If there is none available, you have two reasonable choices:
Top
Look in PhysioToolkit, the repository for
all software available on this site. With very few exceptions, the
software available here is portable among all popular operating systems,
including GNU/Linux, Mac OS X, MS-Windows, and Unix. Since all of it
is provided in source form, you can compile it (using free or proprietary
compilers) into binaries that can run under any of these operating systems.
For convenience, some PhysioToolkit software is also available as
ready-to-run binaries for a variety
of operating systems.
Generally, the same sources can be compiled without modification under any
supported OS or compiler; you will not find separate sets of sources for
different compilers or platforms. Following conventions used by most
free or open-source software, look for files named README or
INSTALL in each software package; these files indicate what's included
in the package, and how to compile it from the sources.
Most PhysioToolkit software is written in portable (ANSI/ISO standard) C.
ANSI/ISO C code can be compiled by all standard C++ compilers. There is a
small amount in other languages, including Fortran 77 and Matlab/Octave m-code.
If you don't have a C or C++ compiler, we strongly recommend the excellent and
free GNU Compiler
Collection (gcc), which includes C, C++, and Fortran 77 compilers (among
others), and is available for a vast range of platforms, including GNU/Linux,
Mac OS X, MS-Windows, and all versions of Unix.
If you wish to write your own software to work with PhysioBank data, the
WFDB library provides standard,
portable interfaces in C, C++, and Fortran for doing so.
The wfdb-swig package provides
Perl, Python, Java, and C# interfaces to the WFDB library. Matlab can use
any of several compatible APIs.
Although it is possible to compile PhysioToolkit software using proprietary
compilers, you are generally on your own if you choose to do so; we don't use
these compilers ourselves, and we can't help you learn how to use them.
Top
Yes. There are two different categories of PhysioToolkit code, and the rules
for using them are slightly different.
The WFDB library is free under the GNU Lesser General Public License
(LGPL). The LGPL permits you to use (or sell, or give away) the library
with your own code. The only significant restriction is that you must make the
sources for the library itself freely available. You do not need to disclose
the sources for your own code simply because you have used the WFDB library
with it.
All of the remaining PhysioToolkit software (the applications) is free
under the GNU General Public License
(GPL). What this means in simple terms is that you can sell it or give
it away to others, but if you do so, you must distribute the sources under the
same terms as those under which you received them.
If you incorporate GPL code into your own code, the resulting code must be
distributed under the GPL or not at all; this is the so-called "viral" property
of the GPL. What this implies is that you cannot simply make minor (or even
major) modifications to free code and then sell it without honoring the
original terms under which you received it.
There are ways to use GPL code together with proprietary code, however.
For example, software that reads output from a GPL program (or that writes data
to be read by a GPL program) does not automatically fall under the GPL. As
another example, you may incorporate GPL code in a plugin for a proprietary
program, but the sources for the plugin itself would have to be made available
under the GPL.
Contributors of software may choose another license conforming to the Open Source
Definition (OSD), so that, in the future, other licenses may apply. Other
OSD licenses have provisions very similar to those outlined above.
Top
First, be sure that it is a bug. Try to reproduce it. Try
doing so on another computer if possible.
If you have not read How to Report Bugs Effectively, please take a few
minutes to do so. (Important: do not send bug reports about PhysioNet to the
author of How to Report Bugs Effectively; he is an innocent bystander.)
Bug reports should provide enough specific information to permit
duplicating your problem. At a minimum, this information includes:
Do not send binary input or output files or core dumps unless requested.
If you can reproduce the problem using input data available on PhysioNet,
please tell us how to do so.
Carefully written bug reports are very valuable to us; we want our
software to work reliably, we are grateful for information that helps
us to fix defects, and we acknowledge the help of those who send us
useful bug reports. If you wish to remain anonymous, please let us know
when you write.
If you are able, by inspection of the sources, to locate the cause of a
problem, tell us what you discover. If you can fix the problem yourself, semd
us a patch against the latest sources. These things, though very much
appreciated, are not essential components of a useful bug report, however; what
is essential is an accurate description of the symptoms of the bug.
In some cases, what we think of as a feature may be what you think of as a bug;
please help us understand what looks wrong to you. Without this context, a
patch may be of little use to us.
All software on this site is provided in source form. If the documentation
for the software in which you have found a bug does not provide an email
address for bug reports, find it at the top of the source file. Please send
all bug reports to both the author/maintainer and PhysioNet.
Top
If you are using a browser such as Netscape or MSIE that supports multiple
windows, links to external sites (URLs that point outside of the PhysioNet
domain) are designed to open the external URL in a separate window. In most
cases, this window will open on top (in front) of the window that contains
the link, but your browser and your window manager or operating system may
override this behavior, especially if the second window was already open and
was hidden. If clicking on a link doesn't seem to do anything, check to see
if there is a second browser window that is hidden behind other windows, or
iconified (minimized, closed).
If you are sure that a link is broken, please send a note about it to
webmaster@physionet.org.
Top
Most of the graphics on PhysioNet, including all of the dynamically
generated graphics, are PNG images. PNG is one of only three
standard image types that are rendered by all modern graphical web browsers,
including Netscape 4.04 and later, and MSIE 4.0b1 and later. The other
supported types are JPEG (which uses lossy compression and is best suited for
continuous-tone graphics such as photos) and GIF (which uses a lossless
compression algorithm that is inferior to PNG's and is not usable in
free software such as the Chart-O-Matic). If you have an obsolete browser,
upgrading it should fix this problem.
Some large images may not fit in your browser window. In most
cases, your browser will display scroll bars that allow you to see
other parts of the image. The QuickTime plugin can interfere with
your browser's built-in capability of rendering PNG images, however.
If you have installed the QuickTime plugin and you follow a link to an
image that is not embedded within an HTML page (for example, by
right-clicking on the image in Netscape and selecting "View image"),
the image will be rendered within your browser window by the plugin,
with results that may be unexpected. Old versions of QuickTime
(including 3.x) display an unscaled image that is cropped if it is
larger than the window, without any scroll bars and with no way to
view the rest of the image. Some later versions of QuickTime (including
4.x) scale oversized images so that they fit in the window, which may
make details hard to see. To avoid these problems, either uninstall
QuickTime, or get an up-to-date version (these problems do not occur
when using QuickTime version 6.0).
Top
PostScript versions of books and papers available here are ready to be printed
on a PostScript printer without any additional formatting. Some users have
experienced problems, particularly with older PostScript versions of the
WFDB Applications Guide (which consists of several PostScript
documents concatenated together into one file). Software that attempts to
insert additional PostScript code, or that attempts to reformat these files
rather than simply printing them as is, is generally the cause of these
difficulties. MS-Windows users can use GSView to view
or print these files. Under UNIX, GNU Linux, or Mac OS X, simply print the
files using lp or lpr, or view them using gv. (Both GSView
and gv require
GhostScript to render PostScript or PDF input.) If your printer has
insufficient memory, it may stop after printing part of the file; in this case,
try using GSView or gv to print the file in sections.
If a PDF version of the file is available here, you may also wish to try
printing it using GSView, gv, or xpdf (all three of these are free and open-source), or
Adobe Acrobat Reader (free binaries, closed-source).
Top
Go back to the beginning of this FAQ and read it
carefully. Still confused? Read on....
Are you looking for something specific? Examples might include:
How can I use Matlab's import feature to read signal files?
How can I use Excel's import feature to read signal files?
rdsamp
What do the sample values represent?
What does the message "init: can't open header for ..." mean?
I can't run rdsamp. Can you please send me a copy of ... in text
format?
How can I get more than a minute of data?
How can I create a PhysioBank-compatible record from my own data?
wrsamp -F 128 -G 102.4 -i data.txt -o Rec01 0
This example reads a text file named data.txt, and creates the files needed for a
record named Rec01, namely, a signal
file named Rec01.dat and a header file
named Rec01.hea. (See What are .dat, .hea, .atr,
.qrs, ... files? for definitions of signal and header files.)
The arguments of -F and -G specify that the signal
was sampled at 128 Hz and that the signal was amplified in such a way that
a step of 1 millivolt would appear as sample values that differ by 102.4
units. The final argument (0) indicates that the leftmost column
in the input (column 0) contains the data.
What do the annotation codes (N, V, S, F, ...) mean?
What is the format of the annotation files?
How can I read annotation files?
What does the error "annopen: can't read annotator ... for record ..." mean?
wfdbwhich 100.atr
If wfdbwhich cannot find the annotation file, copy or move it
into any of the locations in the WFDB path (listed by wfdbwhich),
or add the directory containing the annotation file to the WFDB path. For
further information, see "The
Database Path and Other Environment Variables" in the
WFDB Programmer's Guide.
rdann
What are the columns in rdann's output?
rdann -r mitdb/200 -a atr -t 5
then we obtain this output:
0:00.186 67 + 0 0 0 (B
0:00.625 225 V 1 0 0
0:01.352 487 N 0 0 0
0:01.913 689 V 1 0 0
0:02.677 964 N 0 0 0
0:03.186 1147 V 1 0 0
0:03.980 1433 N 0 0 0
0:04.472 1610 V 1 0 0
Each of these eight lines contains one annotation. The third column shows
the annotation mnemonics, and by referring to the
table of mnemonics.we can see
that the '+' in the first annotation indicates that it marks the
underlying rhythm of the beats that follow; the rhythm type is ventricular
bigeminy, specified by the "(B" that appears in the aux field
at the end of the line; see this
table for descriptions of rhythm annotation strings such as "(B".
The remaining seven lines each mark a QRS complex, associated with either a
normal (N) or premature ventricular (V) beat. Times in the first and second
columns indicate when the events marked by the annotations occur. For example,
the first V beat occurs 0.625 seconds (625 milliseconds), or 225 sample
intervals, after the beginning of the record. (A quick calculation shows that
one sample interval is 2.777... milliseconds for this record, or that its
sampling frequency is 360 Hz. Sample intervals may vary between records.)
The subtyp, chan, and num fields in columns 4, 5,
and 6 are usually zero in reference annotation files, but occasionally one
or more of these fields is used to indicate additional information, as in
this case, in which the subtyp field in the V annotations indicates
which of several ventricular ectopic beat morphologies has occurred. See
the documentation for the associated database to see how to interpret these
fields.
I can't run rdann. Can you please send me a copy of ... in text
format?
How can I create an annotation file?
How can I annotate a record?
I double-clicked on the program icon, and nothing happens!
I typed the program name in the 'Run...' dialog, and nothing happens!What is a "standard input" or a "standard output"?
pour <teapot >teacup
(For an explanation of this command, see the answer to the next question.)
frobnicate <input >output 2>errors
How can I save the output of ... in a file?
How can one program read another's output?
foo >bar
The > operator redirects foo's standard output (which
would normally appear on-screen) into a file named bar. If
bar exists already, its contents are replaced. If you wish to
append foo's output to whatever is already contained in bar,
use a command such as this instead:
foo >>bar
baz <bar
Here, the < operator arranges for baz to read its
input from a file named bar. If bar was created by
foo, then this command allows baz to read foo's
output.
foo | baz
This command runs foo and sends its standard output directly to
baz, without requiring an intermediate file. True multitasking
operating systems such as Unix, GNU/Linux, and Mac OS X allow both programs
to run (apparently) simultaneously; under MS-DOS or MS-Windows, the first
program runs to completion before the second one begins execution.
My question is about WAVE (or gtkwave). Is there a WAVE FAQ?
Yes, look here for answers to
many frequently asked questions about WAVE. The gtkwave project
is no longer active, since WAVE now runs on all of the popular platforms,
including those formerly supported by gtkwave only.
I tried to compile ... but the compiler can't find
wfdb.h (or ecgcodes.h, or ecgmap.h).
I tried to compile ... but the compiler complains
that isigopen (or iannopen, or strtim, or wfdbinit) is undefined.
I'm writing a program to work with PhysioBank data,
but my compiler can't link to the WFDB library. What should I do?
Where on this site can I find software for my
favorite operating system/compiler?
Can I use your code in my commercial application?
How should I report a bug?
Some links don't work, but I don't see any error.
Why not?
I'm having trouble viewing images on this site.
Why?
I'm having trouble printing PostScript files from this site. Why?
I don't understand how to use the software or data
on this site.
If so, use PhysioNet's search facilities. All
text on this site is indexed.
Have you found something relevant to your interest, but don't know how to use it? If so, look for tutorial materials that can help you get started. Browse through PhysioNet's list of tutorials, or use a PhysioNet search to find information to help you get started.
PhysioNet Discussions are also useful resources if you are unable to find answers to your questions elsewhere on the site. The discussion archives are indexed and are included in PhysioNet searches, so please do a search to see if your question has already been asked and answered before posting it.
Before posting, please formulate specific questions ("I don't understand how to use the data." or "The software doesn't work, please help me!" are examples of non-specific questions that cannot be usefully answered). Whoever replies to your question cannot read your mind; if you don't say clearly what you need to know, you will not get a satisfactory answer.
Unless your question is of no possible interest to other users, we encourage you to post it in the relevant discussion group if you can't find an answer after making a reasonable effort to do so. If you prefer, you can write to the address at the bottom of this page (note that all discussion group postings are also sent to this address, so it is unnecessary to send an additional copy).
If you have a question about a specific page in the PhysioNet web site, click on the "webmaster@physionet.org" link at the bottom of that page; doing this opens a preaddressed email window, with the URL of the page filled in as the subject, which will help us to understand the context of your question and to give you a relevant answer.
Don't be offended if the reply to your question is "Read the FAQ!" If the answers aren't there, or if they aren't clear, write again, and try to be more specific, or to point out what's confusing or missing in the FAQ. Doing so will not only help you to get a useful answer, but it will also help us to write a better FAQ.
A man page is a concise description of how to use a piece of software, intended to be read using man or one of its work-alikes. Think of man pages as pages from a reference manual.
All Unix platforms, including GNU/Linux and Mac OS X, as well as Cygwin/MS-Windows, include a program called man that can be used to find and display man pages. This is the standard form of documentation for all Unix software. Almost all PhysioToolkit applications have man pages. The near-universality of man pages means that you are very likely to be able to learn about any program by typing its name as an argument to a man command, as in:
man tar
which will display the man page that describes the standard
tar command. On most platforms, the output of man is sent
through a program such as more, which allows you to read it one
screenful at a time; you may usually advance to the next screenful by pressing
the space bar, go back a screenful by typing 'b', or exit by typing 'q'.
The format of man pages is fairly rigid, which allows a variety of software to extract useful information from them for purposes of indexing, cross-referencing, etc. They are not intended as tutorial material, but once you are familiar with their format, reading them is usually the quickest way to learn how to use the software they document.
The largest collection of man pages on PhysioNet is the WFDB Applications Guide, which includes not only the man pages for the roughly 60 applications in the WFDB Software Package, but also those for a number of contributed applications that are compatible with WFDB Software. These pages can be read within your web browser; if you download and install the WFDB Software Package on your own computer, you can use man to read the local copies of these man pages that will be installed together with the software itself.
A distinctive feature of PhysioNet's man pages is the Sources section at the end of each one, with one or more URLs that give the location of the software sources. This feature is particularly handy if you are reading a man page in your web browser and would like to refer to the source of a program in order to see how it is implemented.
The Computer Science Department of McGill University offers a gentle introduction to reading man pages that will help you get started if you haven't used man pages previously.
Although you won't find the acronym "RTFM" used elsewhere on this site, it refers to the usefulness of Reading The Fine Manual (i.e., the man pages) to inform yourself about software that may be unfamiliar. Try it!
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Updated Friday, 16-May-2008 14:47:23 EDT