Complete Implementation of Pan Tompkins;
If you found this script useful please cite the following references;
%% References :
%[1] Sedghamiz. H, "Matlab Implementation of Pan Tompkins ECG QRS detector.", March 2014. https://www.researchgate.net/publication/313673153_Matlab_Implementation_of_Pan_Tompkins_ECG_QRS_detect
AND
%[2] PAN.J, TOMPKINS. W.J,"A RealTime QRS Detection Algorithm" IEEE
%TRANSACTIONS ON BIOMEDICAL ENGINEERING, VOL. BME32, NO. 3, MARCH 1985.
%% Author : Hooman Sedghamiz
% Linkoping university
% email : hoose792@student.liu.se
% Copyright march 2014

%% Method :
%% PreProcessing
% 1) bandpass filter(515 Hz)
% 2) derivating filter to high light the QRS complex.
% 3) Signal is squared.
% 4)Signal is averaged of noise (0.150 seconds length).
% 5) depending on the sampling frequency of your signal the filtering
% options are changed to best match the characteristics of your ecg signal
%% Decision Rule
% At this point in the algorithm, the preceding stages have produced a roughly pulseshaped
% waveform at the output of the MWI . The determination as to whether this pulse
% corresponds to a QRS complex (as opposed to a highsloped Twave or a noise artefact) is
% performed with an adaptive thresholding operation and other decision
% rules outlined below;
% a) FIDUCIAL MARK  The waveform is first processed to produce a set of weighted unit
% samples at the location of the MWI maxima. This is done in order to localize the QRS
% complex to a single instant of time. The w[k] weighting is the maxima value.
% b) THRESHOLDING  When analyzing the amplitude of the MWI output, the algorithm uses
% two threshold values (THR_SIG and THR_NOISE, appropriately initialized during a brief
% 2 second training phase) that continuously adapt to changing ECG signal quality. The
% first pass through y[n] uses these thresholds to classify the each nonzero sample
% (CURRENTPEAK) as either signal or noise:
% If CURRENTPEAK > THR_SIG, that location is identified as a “QRS complex
% candidate” and the signal level (SIG_LEV) is updated:
% SIG _ LEV = 0.125 ×CURRENTPEAK + 0.875× SIG _ LEV
% If THR_NOISE < CURRENTPEAK < THR_SIG, then that location is identified as a
% “noise peak” and the noise level (NOISE_LEV) is updated:
% NOISE _ LEV = 0.125×CURRENTPEAK + 0.875× NOISE _ LEV
% Based on new estimates of the signal and noise levels (SIG_LEV and NOISE_LEV,
% respectively) at that point in the ECG, the thresholds are adjusted as follows:
% THR _ SIG = NOISE _ LEV + 0.25 × (SIG _ LEV ? NOISE _ LEV )
% THR _ NOISE = 0.5× (THR _ SIG)
% These adjustments lower the threshold gradually in signal segments that are deemed to
% be of poorer quality.
% c) SEARCHBACK FOR MISSED QRS COMPLEXES  In the thresholding step above, if
% CURRENTPEAK < THR_SIG, the peak is deemed not to have resulted from a QRS
% complex. If however, an unreasonably long period has expired without an abovethreshold
% peak, the algorithm will assume a QRS has been missed and perform a
% searchback. This limits the number of false negatives. The minimum time used to trigger
% a searchback is 1.66 times the current R peak to R peak time period (called the RR
% interval). This value has a physiological origin  the time value between adjacent
% heartbeats cannot change more quickly than this. The missed QRS complex is assumed
% to occur at the location of the highest peak in the interval that lies between THR_SIG and
% THR_NOISE. In this algorithm, two average RR intervals are stored,the first RR interval is
% calculated as an average of the last eight QRS locations in order to adapt to changing heart
% rate and the second RR interval mean is the mean
% of the most regular RR intervals . The threshold is lowered if the heart rate is not regular
% to improve detection.
% d) ELIMINATION OF MULTIPLE DETECTIONS WITHIN REFRACTORY PERIOD  It is
% impossible for a legitimate QRS complex to occur if it lies within 200ms after a previously
% detected one. This constraint is a physiological one – due to the refractory period during
% which ventricular depolarization cannot occur despite a stimulus[1]. As QRS complex
% candidates are generated, the algorithm eliminates such physically impossible events,
% thereby reducing false positives.
% e) T WAVE DISCRIMINATION  Finally, if a QRS candidate occurs after the 200ms
% refractory period but within 360ms of the previous QRS, the algorithm determines
% whether this is a genuine QRS complex of the next heartbeat or an abnormally prominent
% T wave. This decision is based on the mean slope of the waveform at that position. A slope of
% less than one half that of the previous QRS complex is consistent with the slower
% changing behaviour of a T wave – otherwise, it becomes a QRS detection.
% Extra concept : beside the points mentioned in the paper, this code also
% checks if the occured peak which is less than 360 msec latency has also a
% latency less than 0,5*mean_RR if yes this is counted as noise
Hooman Sedghamiz (2020). Complete Pan Tompkins Implementation ECG QRS detector (https://www.mathworks.com/matlabcentral/fileexchange/45840completepantompkinsimplementationecgqrsdetector), MATLAB Central File Exchange. Retrieved .
1.8   Cleaned up the code.


1.7.0.0  % Citations added 

1.7.0.0  Delay Bug removed. 

1.6.0.0  Fixed the bug with ax handles! 

1.10.0.0  Filters Impulse responses got fixed! 

1.10.0.0  Bug in findpeak fixed to handle different sampling freqeuencies 

1.9.0.0  description updated 

1.8.0.0  a flag added to have an option for skipping the plots (the name of the variable is 'gr') 

1.7.0.0  the description for the variable Delay added 

1.6.0.0  better plots 

1.5.0.0  Script enhanced and tested on several MITBIH arrhythmia database, results are very close to the ones in the paper, tested on tape no. 100,101,102,104,222,234 

1.4.0.0  There was a bug in the script which was removed round(0.100*Fs) changed to round(0.150*Fs) 

1.3.0.0  Better plots added and some bugs removed 

1.2.0.0  Filtered cut off frequency enhanced 

1.1.0.0  Edited description 
Inspired by: An online algorithm for R, S and T wave detection, Toolbox for unsupervised classification of MUAPs and action potentials in EMG
Inspired: BioSigKit a toolkit for BioSignal analysis, An online algorithm for R, S and T wave detection
Create scripts with code, output, and formatted text in a single executable document.
Thank you for sharing this, I am studying biomedical engineering and have just covered this algorithm in my course on Biomedical Signal Processing, I am having some trouble understanding the adaptive thresholding process and would appreciate any help if you could provide an explanation to simplify it for me. Thanks again,
Paavan
Thanks a lot Sedghamiz, a quick question, i have a nocturnal ECG recording where the signal amplitude drops suddenly, possibly due to body posture. The algorithm is unable to adapt the threshold and rejects the section with low amplitude. What would be the best way to resolve this issue?
Hi, small question
No matter what size of vector of ECG I enter the result of the R indexes stays the same. I mean the size of the vector R which represents the indexes of R is always 167. how i can solve it? i don't understand the source of the problem
nice!
Thanks a lot Mr. Sedghamiz.
Can anyone tell me How to find FN and FP?
different filtering criteria is applied if the ecg sampling frequency is not 200. . Why
good work
thank you very much for this code .. I want to know how we can evaluate the qrs detector means calculate the sensitivity and accuracy of detection?
thanks
not working
With the records throws low sensibility and predictivity:
Sensibility Predictvity
108m 50,9937% 42.74155%
207m 12.3659% 10.37438%
217m 31.29529% 31.323663%
What can be done to increase sensitivity and predictivity?
i am geetting following error
"Not enough input arguments.
Error in pan_tompkins (line 43)
if ~isvector(ecg)"
how to fix it?
Is it possible to detect the pwave
Can I translate to java language?
why it always show me this?
Error using pan_tompkin (line 47)
ecg must be a row or column vector
i use ecg signal from physionet.org
Hi! I get a really weird error when I try and use this;
Error using findpeaks
Too many output arguments.
Error in pan_tompkin (line 156)
[pks,locs] = findpeaks(ecg_m,'MINPEAKDISTANCE',round(0.2*fs));
Any ideas?
Seems great but, could you add an output with the samples corresponding to the RPeaks?
For more algorithms in regards to ECG analysis and QRS and T wave detection, see my recent submission BioSigKit:
https://www.mathworks.com/matlabcentral/fileexchange/67805biosigkitatoolkitforbiosignalanalysis?s_tid=prof_contriblnk
Hooman,
Many thanks for the algorithm. It works perfectly for peak detection. Is there any way to use this algorithm to find out pulse train with index of R peaks?
Thanks hooman for this code. But it is not working properly with MITBIH 101 record. I have one query how to get those variables which contain all the outputs. Here only one variable is appearing after a successful run that is 'ans'. Please tell how to get the other variables which contain peak locations...etc... Please help...
this program is not detecting correct R peaks in case of MITBIH normal sinus rhythm database. can you please suggest any changes required in this function file so that correct R peaks should be detected. sampling frequency is set at 360 hz. please help
Guys how to load my dataset in this code ???plss help
Thanks a lot Mr. Sedghamiz.
How do you suggest finding the peaks without using a built in function such as 'findpeaks'.
Is this a full feature extractor?
Hello Mr. Sedghamiz. H, first of all thank you very much for sharing these codes and congratulations for all your work. I wanted to ask : why do you take 0.25 of the max amplitude to calculate THR_SIG during the learning phase 1, is it from Pan Tomkins paper ? Then, you say 0.25 of the max amplitude but your formula is : THR_SIG = max(ecg_m(1:2*fs))*1/3. Is it a mistake ?
In advance, thank you very much !
hello thx for your job! its very kind of u to share those codes. but I have one question to ask .how to define the frequency of ECG samples? when I want to use my own data ,looking forward to your response thank u!!
I've implemented this code up till the filters but I'm having trouble with implementing the thresholding part.
what I don't understand is what to initialize the following variables with?
qrs_c =[];
qrs_i =[];
nois_c =[];
nois_i =[];
qrs_i_raw =[];
qrs_amp_raw=[];
SIGL_buf = [];
NOISL_buf = [];
THRS_buf = [];
SIGL_buf1 = [];
NOISL_buf1 = [];
THRS_buf1 = [];
A quick response will be highly appreciated. and Thanks in advance.
I'm using a sleep apnea ECG signal for a project. I want to use this for R peak detection however would the filtering of this code work for this type of signal? I assume the filtering was meant for a standard ECG signal with some noise.
i'm new to matlab and i'm wondering about the input! how can i import data from the data base MITBIH and use as input for this script? what are the commands?
and thx
To elaborate on my comment
I seem to think that
int_c = (51)/(fs*1/50) is a more reasonal
interpolation technique to get new derivative filter, any thoughts?
I have a problem understanding
int_c = (51)/(fs*1/40);
b = interp1(1:5,[1 2 0 2 1].*(1/8)*fs,1:int_c:5);
dont know how it modifies the fs to the derivative filter, thats for the code!!!
thanx for a code but when I run it find an error like Not enough input arguments.(line 118) please help me.
thanks for your code
but when i run it i find this error
pan_tompkin(ecg, fs, gr)
Error using ecg (line 22)
Not enough input arguments.
Thanks a lot for the code, but it seems not work well for the data MITBIH 114 record, missing too many peaks, please check.
please I'm waiting for your help regarding my last question?
Thanks a lot for this code, its run with your sample data.I'm new to matlab, I need a help, my ECG in mat format taken from physionet, which is much longer. how I can make this code work with such longer ECG signal. Also, How I can find the value for R peaks, and how to calculate RR interval using this algorithm. PLEASE HELP !
Excellent! Ran a couple of data files through hasn't missed a beat so far, no pun intended. Great job!
Thanks a lot for proper implementation of Pan Topkins. Now, once we get index of detected Rpeak, we can detect entire qrs complex, some samples to right and to left, of R peak. So, what is the number of samples to detect qrs complex?
Okay, it has come to my attention that the Matlab implementation of original filters proposed in PanTompkins paper do not achieve a bandpass of 512 Hz. Anyways, I have them in the script commented in case one wants to use it. Any ideas on this welcome :)
The delay is now not properly initialized (uncomment line 134?).
Greetings, David
Giorgia and Israel you are right. The impulse response of the highpass filter was wrong.Just updated them. The issue with the ax handles also fixed. Soon I will be uploading a version that does not use any built in functions in matlab such as findpeaks and would be really similar to a real time implementation.
Thanks for the feedback!
Israel Yohannes I agree with you. I can't understand why the filter's coefficients are:
b = [1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 32 32 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1];
a = [1 1];
and not:
b = [1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1];
a = [1 1];
Can i detect PQ,QP,RT,TR,PS and SP using this algorithm please guide asap.
Thanks
Hello, it appears that this is no longer working under the current version R2016b. I'm not sure when the changes happened. The fix is easy though.
The error I received was:
>> [qrs_amp_raw,qrs_i_raw,delay]=pan_tompkin(S1B_r1_ekg, 1000);
Conversion to logical from matlab.graphics.Graphics is not possible.
Error in pan_tompkin (line 434)
if ax(:)
This seems to be related to the fact that graphics handles are now objects, not doubles:
https://www.mathworks.com/help/matlab/graphics_transition/graphicshandlesarenowobjectsnotdoubles.html
I was able to correct this by adding isgraphics(ax(:)) on line 433. After that change, the function runs without error.
is the high pass filter coefficients correct??
code :
b = [1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 32 32 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1];
a = [1 1];
I thought it should be
b = [1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1];
a = [1 1];
@nur, 1x25 means the code detected 25 peaks. 1st matrix will show those 25 amplitudes and the second matrix will show their position(index). The third variable is the delay.
Does not work for some signal. I am trying to find the problem.
i have a question on how can i determine the r peaks value? for example, did it been saved on the workspace as 'ans'? bcoz it just give me a column of value, (to be exact 1X25 in matrix) and i dont know the purpose of the value. thanks. i'm still a beginner and really want to know how this work expecially on this code function [qrs_amp_raw,qrs_i_raw,delay]=pan_tompkin_revised(ecg,fs,gr)
good job, thx a lot
helps a lot ,thx
thx
thanks!
very good
thanks so much, but I have an Error in this line
[pks,locs] = findpeaks(ecg_m,'MINPEAKDISTANCE',round(0.2*fs));
How can I resolve it
Thanks a lot!
The program looks really good, but I get this error:
Conversion to logical from matlab.graphics.Graphics is not possible.
Error in pan_tompkin (line 433)
I am calling the function from a script with the following line:
[qrs_amp_raw,qrs_i_raw,delay]=pan_tompkin(x,fs);
where x is my signal and fs is the sample frequency.
Any idea on what could be wrong? It is an EOG signal, not an ECG, so it is slightly different, but it should work for finding the QRS, I think. Thank you in advance for your help.
this programm works good!!
Hi, I am new to matlab. Is there anyone who can tell me how to execute this program?
i tried to insert the function at the first line as follow:
pan_tompkin('ecg.txt',360,1);
it couldnot run. Help please
it is very helpful
and i want to calculate the heart rate how can i do it as this algorithm gives 2 heart rate ... how can i solve this problem ??
It helps me a lot.
But i have a small problem, when i tried data which is a vector of 74 points ... I got this error
Error in ==> pan_tompkin at 230
THR_SIG = max(ecg_m(1:2*fs))*1/3; % 0.25 of the max amplitude
any help?
Pan Tompkins algorithm is showing the QRS amplitude, but however it is not indexing 'R' peak. could any say how find the index of 'R' index
Hi... Your code runs very well.
A little HELP required..!!!!!
Please tell me the formula to calculate the HEART RATE of the input ecg signal.
Please provide a prompt reply.
THANKS..!! :)
Hi Hooman,
Quick question. On lines 212 and 213 you have:
ecg_m = conv(ecg_s ,ones(1 ,round(0.150*fs))/round(0.150*fs));
delay = delay + 15;
But isn't that delay amount only valid for the case when fs = 200? When using other sampling frequencies the moving average will have a different length and hence a different delay. Wouldn't this be better:
delay = delay + round((0.150*fs)/2);
Hooman, great work and great code!
Could you help me with one question: which algorithm is better in your opinionclassic Pan and Tompkins or modified HamiltonTompkins approach?
Are you going to write the implementation in Matlab for HamiltonTompkins algorithm?
Cheers, Alex!
At line 233:
[pks,locs] = findpeaks(ecg_m,'MINPEAKDISTANCE',0.2*fs);
'MINPEAKDISTANCE' must be integer, otherwise we will get error:
Error using findpeaks>parse_inputs (line 77)
MinPeakDistance should be an integer greater than 0.
Error in findpeaks (line 43)
[X,Ph,Pd,Th,Np,Str,infIdx] = parse_inputs(X,varargin{:});
Error in pan_tompkin (line 233)
[pks,locs] = findpeaks(ecg_m,'MINPEAKDISTANCE',0.2*fs);
So you can use:
[pks,locs] = findpeaks(ecg_m,'MINPEAKDISTANCE',round(0.2*fs));
Worked well for me, except for signals with sporadic high noise, like this one: https://drive.google.com/file/d/0B0oLTmfsFF6sSk5UeFBGTDNPSWc/edit?usp=sharing
Why on line 340 is used this inequality?
if length (qrs_c)> = 3
Hello, Hooman Sedghamiz! I apologize for my English. Thank you for your work
and the possibility to meet her. I want to fully understand the workings of
the algorithm. I is hard to do on the provided you file because it is made as
universal. Therefore, I ask you about the option of an algorithm in a more simple
way to understand. For example only for the 200 Hertz, etc.
'll Be very happy if you give me a simple option for analysis.
Sincerely.
P.S. Can I find it easier to write in Russian?
@Govind, Good point. Well, I guess I added that part cause the whole Slope analysis idea in the original paper was not performing very nice and was not able to distinguish the T wave. I just added that extra part to handle the issue but its better to remove it. In my free time, I plan to enhance the code by adding the Hamilton algorithm peak detector that can increase the accuracy to some extent. will be come up soon.
Cheers
I think you need to add the option 'valid' when doing convolution
Thanks for the great code. I've been running it on some real signals and I found that there might be a problem with the "Extra concept: this code also
checks if the occured peak which is less than 360 msec latency has also a
latency less than 0,5*mean_RR if yes this is counted as noise"
It causes some peaks to be missed especially if the signal has PAC. As an example see
signal:
http://i.imgur.com/kqyERvu.png
default behavior:
http://i.imgur.com/LLjOn5m.png
" (locs(i)qrs_i(end)) <= round(0.4*test_m)" commented out:
http://i.imgur.com/OQVqDW5.png
ok. Done now you can use this function as an internal function by muting the plots. Just set the last input 'gr' equal to 0 .
Good, that's what I had thought. One other suggestion: it would be nice to be able to just set a flag parameter as to whether or not the graphs should be plotted, or whether it should be done silently.
thanks Kyle. delay is a variable showing the number of samples where the signal is delayed due to the filtering. I added the description to the file.
Excellent algorithm implementation, thank you for this. Would you mind adding a description for the "delay" output variable? I have an idea of its purpose, but would like to make sure I'm accurate.
Thank you very much for your time! At the beginning I ignored the second channel
There were some small bugs that i fixed today, i guess it will work much better now. thanks for your feedback :)
my bad,sorry, i made a mistake in importing the ecgs from physionet, they are much longer.I just analyzed 83 seconds of each,of course they are longer .
So, I just finished testing some of your database on the algorithm, it is highly correlated to the results in the paper, here are the outcomes : Tape no 100, 102, 103,231 detected all the beats without any false negative and false positive,100% detection as reported in the paper. As it says in the paper, they had problem with the tapes number 108 and 222 and they had 12.54% and 7.33% failed detection where after applying my script on tape 108(channel 1) i got 10 false detections where if you divide it by the reference number of beats in this tape (channel 1), you get 11.76(which is close to 12% in the paper), and in tape 222 i got 8.57% (which is again correlated to 7.33%). I think these samples in physionet are not the complete tapes used in Pan tompkins, since if you check the paper for examples, in tape 222 they had 2484 beats in total, however, in the version in physionet there is just 105 of that 2484 beats. I think this causes the slight difference in the results they reported in their paper and the outcome of this script :). Also, note that some of the channels in some tapes are totally distorted, in that case use the other channel.
cheers,
Hooman
Thanks for your feedback. I tried the resampling function (also with different n) but never came close to the values shown in the paper.
@AR thanks for your comments. In the code, the filtering options are different based on the sampling frequency, but if you use an ECG with 200Hz sampling frequency it will be processed with exactly the same filters described in Pan tompkins. If you have a signal with different sampling frequency and you dont want to use other filtering options, another idea would be to use the Resampling function in matlab which can convert whatever sampling frequency to 200Hz it uses FIR filters to do so but still your signal might be distorted however you can minimize this by choosing a larger n in resampling function. read more here;
http://www.mathworks.de/de/help/signal/ref/resample.html
another suggestion would be to change all
round(xyz*fs)
with
2*round(((xyz*fs)+1)/2)1;
to get an odd number of samples
In the %% Thresholding and online desicion rule %% section you should replace:
if locs(i)round(0.100*fs)>= 1 && locs(i)<= length(ecg_h)
with
if locs(i)round(0.150*fs)>= 1 && locs(i)<= length(ecg_h)
When working with the MITBIH Arrhythmia Database from PhysioNet (as mentioned in the paper from Pan & Tompkins) you get different results (worse than proposed). Of course the sampling frequency is different...
Concerning one question I received by email; this script is able to handle all different sampling frequencies. That line of the code ''rem(fs,200)*fs/200 '' is to make sure that if your sampling frequency is higher than 200 Hz and dividable to 200Hz then the code downsamples your signal to 200 Hz for example if your sampling frequency is 400Hz or 600Hz or 1000 Hz it automatically downsamples it to 200Hz and then uses the original filters introduced in Pan tompkins algorithm which are suitable for 200Hz sampling frequency. If you sampling frequency is not dividable to 200 Hz for example as you said if it is 360Hz then the code uses another filtering option for such a frequency which is a bandpass butterworth filter with a bandpass equal to filters in Pan tomkins paper which was 0.515 Hz. Therefore, based on the sampling frequency the type of the filters vary but this is done automatically in the code and you dont need to do it yourself.
for a more simple peak detector check out my other R, S, and T wave detector.
http://www.mathworks.com/matlabcentral/fileexchange/45404ecgqrswaveonlinedetector