How can I subtract the baseline to zero?
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I need to compare peak heights of several spectra but they do not baseline at zero, is there a way I can revert the baseline to zero using code on MATLAB?
Thanks, Hannah (absolute matlab novice)
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Accepted Answer
Image Analyst
on 16 Jan 2015
If you have the Signal Processing Toolbox you can use a Savitzky-Golay filter and I've attached a demo for that, or medfilt1(). Or if you have the Curve Fitting Toolbox you can use smooth() or lowess() or rloess() or functions like that. (Not sure if I spelled them correctly since I don't have that toolbox.
Attach your data and tell us what toolboxes you have and you might get someone to write you some code.
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Image Analyst
on 18 Jan 2015
Hannah, I don't know what variables you're talking about, but true, about half my code is to just synthesize data because you didn't supply me with any. The main code is just these two lines:
baselineY = sgolayfilt(y, polynomialOrder, windowWidth);
detrendedY = y - baselineY;
Everything else is just to make it fancy or initialize things.
I chose an order of 3 because the curve sort of looked like a sine wave which has orders 1, 3, 5, etc. if you know the Taylor series form of it. But really for the Savitzky-Golay filter you don't want too high an order because it just takes more time and doesn't improve the results any. If you make a higher order it will just follow the noisy wiggles more and you don't want that . A lower order like 1, 2, or 3 will give better smoothing.
More Answers (4)
Matt J
on 16 Jan 2015
If you have the Image Processing Toolbox, maybe a median filtering would give a good approximation of the baseline, e.g.,
X-medfilt2(X,[1,3])
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Muhammad Irfan
on 30 May 2016
I never thought I could easily find the solution to this problem :)...thanks Hannah and image analyst..
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Muhammad Irfan
on 30 May 2016
Hi image analyst,...could you kindly advise which filter would work with my signal below..im having difficulties with using the filter u suggested to hannah...
thanks a lot in advance
1 Comment
Ella
on 20 Feb 2017
Dear Image Analyst,
Thank you for your help with Hannah's question. I tried this method with my data and obtained a flat line. I was wondering if you might be able to help me out with a general baseline removal. In case this is possible, I have attached an example spectrum in .txt format (TanX and TanY are to be plotted on the x and Y axis and are one above each other in the document). We're only concerned about the peaks which are obvious. It was an x-ray photo-electron spectroscopy measurement. Thank you very much!!
4 Comments
Image Analyst
on 23 Feb 2017
Since you didn't start your own question, I couldn't answer it, but you can still give me the same number of reputation points (2) by "Voting" for my answer to Hannah up above (below my avatar). It doesn't matter that it was not directed towards you. Thanks for considering that!
Ella
on 23 Feb 2017
Ah I see! Actually I already voted for your answer when I read it first time because it was the closest I had got to something useful! Okay - then if I have another question one day I'll post it in a seperate question then. Thanks again.
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