After reading MITDB ECG annotation files using the Matlab wrapper for WFDB, I get five columns. The first is the time interval and the third seems to be the beat type. I assume fourth and fifth refer to the beat being detected or not in each of the two leads. Is it correct?
I cannot find any documents explaining the annotation contents. So, my question is: which beats must be taken into account to validate a QRS complex detector?
Annotations are explained in this site: https://physionet.org/physiobank/annotations.shtml
The output of the rdann function is found here:
https://physionet.org/physiotools/matlab/wfdb-app-matlab/html/rdann.html
I assume to validate a QRS detector you will need to get rid of all "non-beat" annotations, and the remaining annotations will be the correct heart beats?
Thanks!
Now I see that what confused me was that the Matlab WFDB implementation adds 1 to the annotation type. For example, a normal beat is annotated as 79 (which is char 'O') instead of 78 (char 'N').
As for validating, the question that remains is which valid beats have to be used. I mean: annotated beats are not always over the R peak. Some of them are on the S wave (in rS situations). Do I have to check if an annotation is an S "valley" or an R "peak" manually?
I see in some papers that Pan Tompkins algorithm surpasses the 99% hit rate with MITDB, and I am unable to reproduce this result (with Pan and Tompkins). So, obviously I am not checking the proper annotated beats.
Also: what is the maximum time difference from detected beat to the annotated beat to consider it correct?
Regards!
I'm not sure if there is a way to automatically exclude annotations that are not R peaks. I think you just need to exclude every char that is listed under the "non-beat annotations".
I think it is up to you to determine how close two beats need to be for it to be considered correct, however the minimum possible time between two heartbeats is 0.2 seconds (I don't have a reference for this unfortunately), so this might be a good starting point.
Dear Dr. Antoni
Did you find how to read MIT-BIH ECG annotation files?
Can you share with me because i also want to know how to validate R peak with annotated beats.
Thank You
I know its a late response. Hopefully it will help somebody else.
Since MIT-BIH record's annotation files are of the .atr format, the below code will do the job.
ann_ref = wfdb.rdann (record_path,'atr')
Is there any standard for what beats to use?
Mark Gardner, as you pointed out, I believe we have to remove the 'non-beat' annotations. But, within the beat-annotations, should we consider them all? E.g. unclassifiable beat, premature ventricular contractions..?
Are there any QRS validation guidelines?
Thank you
There are guidelines defined by this standard: ANSI-AAMI-EC13 and if you go to section 5.1.2.1 they have some example waveforms and how to treat them (I think you can find a free version somewhere). These waveforms are available on Physionet (https://physionet.org/content/aami-ec13/1.0.0/).
I think (incoming personal opinion) that abnormal heartbeats such as premature ventricular contractions are counted when detecting heartbeats.
The "rdann" function in WFDB Toolbox for MATLAB can be used to read the annotation file (https://www.physionet.org/physiotools/wag/rdann-1.htm).
[ann,anntype]=rdann('mitdb/100','atr');
The "ann" variable contains timestamp data while "anntype" contains annotation type as a character.
Documentation of "rdann" can be found here (https://archive.physionet.org/physiotools/matlab/wfdb-app-matlab/html/rdann.html).
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