[Mne_analysis] Badly resample signal_ Magnitude clipping

Thu Aug 22 22:31:12 EDT 2019

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Dear Phillip,

I resampled a signal that originally sampled at 1000Hz to a different frequency (i.e., 1000Hz, 800Hz, 100Hz). The three figures that attached with this email showed different sampling rate results in different magnitude for the signal at the same time.

I understand from your explanation that this is expected where resampling will result in lose of temporal resolution, so fast, high amplitude deviations are lost. But I notice from my experimentation; the amplitude deviation occurs throughout the resampled signal. Because of this, I am concern whether I performed the whole procedure properly or not. FYI, I would like to resample the signal into 100Hz.

The figure can be reproduced using the notebook that accessible from this link<https://github.com/balandongiv/EyeCloseOpen/blob/master/HelpImportDownsample_EDF.ipynb>

Dear Sebastion
Thanks for the reply. Yes, it is about Nyquist Theorem. Thanks for the explanation, I really appreciate it.

Regards
Rodney

From: Sebastián Castaño-Candamil <sebastian.castano at blbt.uni-freiburg.de>
Sent: Thursday, 22 August, 2019 5:13 PM
To: Discussion and support forum for the users of MNE Software <mne_analysis at nmr.mgh.harvard.edu>; RODNEY PETRUS BALANDONG <rodney.petrus_g03291 at utp.edu.my>
Cc: Phillip Alday <phillip.alday at mpi.nl>; mne_analysis at nmr.mgh.harvard.edu
Subject: Re: [Mne_analysis] Badly resample the signal

Hi Rodney,

there isn't a way around that, i.e., it is a theoretical limitation, (I dont know exactly your background, and apologize in advance in case you already know this, but:) you cannot represent frequency components wit a frequency > Fs/2, where Fs is your sampling frequency. In your case, you cannot analysis parts of the signal beyond 50Hz if you sample at 100

I do not know exactly what is the frequency of those fast variation, but I'd think that these are above 50ish Hz.

Hope that helps,
Sebastián

Sebastian Castaño-Candamil
Doctorate student
Brain state decoding lab
University of Freiburg
E // sebastian.castano at blbt.uni-freiburg.de<mailto:sebastian.castano at blbt.uni-freiburg.de>
On Aug 22 2019, at 10:59 am, RODNEY PETRUS BALANDONG <rodney.petrus_g03291 at utp.edu.my<mailto:rodney.petrus_g03291 at utp.edu.my>> wrote:

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I only interested with the signal up to 100Hz, so it redundant and computationally expensive to handle signal with 1000Hz.

I'm just curious whether ignoring those brief high-frequency peaks will affect the overall analysis later.  So, if  there is a way to these brief high-frequency would be an advantage.

Anyhow, is it common practice to neglect the brief high-frequency peaks?

From: Phillip Alday <phillip.alday at mpi.nl<mailto:phillip.alday at mpi.nl>>
Sent: Thursday, 22 August, 2019 4:53 PM
To: RODNEY PETRUS BALANDONG <rodney.petrus_g03291 at utp.edu.my<mailto:rodney.petrus_g03291 at utp.edu.my>>
Cc: mne_analysis at nmr.mgh.harvard.edu<mailto:mne_analysis at nmr.mgh.harvard.edu>
Subject: Re: [Mne_analysis] Badly resample signal

But why do you need to resample? That's what I meant with an XY problem.

Why do you care about brief high-frequency peaks?

Phillip

On 22/08/2019 11:46, RODNEY PETRUS BALANDONG wrote:
I need to downsample an original signal that sampled at 1000Hz to 100Hz.

From: Phillip Alday <phillip.alday at mpi.nl><mailto:phillip.alday at mpi.nl>
Sent: Thursday, 22 August, 2019 4:44 PM
To: RODNEY PETRUS BALANDONG <rodney.petrus_g03291 at utp.edu.my><mailto:rodney.petrus_g03291 at utp.edu.my>
Cc: mne_analysis at nmr.mgh.harvard.edu<mailto:mne_analysis at nmr.mgh.harvard.edu>
Subject: Re: [Mne_analysis] Badly resample signal

Appropriate filtering may help with some things, but .... I think we're heading into XY question territory here (http://xyproblem.info/).

Why do you want to resample? What are you trying to accomplish?

Phillip

On 22/08/2019 11:38, RODNEY PETRUS BALANDONG wrote:
Dear Phillip,

Thanks for the response,

Just wonder whether there exist different technique to address such an issue? For example, rather than using the averaging approach

Regards

Rodney

From: Phillip Alday <phillip.alday at mpi.nl><mailto:phillip.alday at mpi.nl>
Sent: Thursday, 22 August, 2019 4:33 PM
To: Discussion and support forum for the users of MNE Software <mne_analysis at nmr.mgh.harvard.edu><mailto:mne_analysis at nmr.mgh.harvard.edu>; RODNEY PETRUS BALANDONG <rodney.petrus_g03291 at utp.edu.my><mailto:rodney.petrus_g03291 at utp.edu.my>
Subject: Re: [Mne_analysis] Badly resample signal

This is expected behavior for resampling. With resampling, you lose temporal resolution, so fast, high amplitude deviations are lost.  This is what happens at the beginning of your signal. Later in the signal you see that the slower change in the mean of the signal is preserved, but the bumps are list.

Intuitively: you have fewer samples, so you can't capture both the deviations up and the deviations down, so they average out and you get just the mean. So the big peak and big trough early in your example just cancel out when resampled.

Phillip

On 22/08/2019 07:01, RODNEY PETRUS BALANDONG wrote:
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Dear All,

The issue is about sample badly approximated

Given an original signal sampled at 100Hz, the objective was to downsampled it into 50 Hz

The downsampling process was realised using the MNE resample.

However, as can be noticed from the image below, the sample is badly approximated. Instead of registering the original signal magnitude, the function RESAMPLE return an approximated signal magnitude.

This rise two question

  1.  Is it common for such badly resample to occur?

  1.  If yes, how to minimize this

The problem can be reproduced using the notebook which is accessible through this link<https://github.com/balandongiv/EyeCloseOpen/blob/master/HelpImportDownsample_EDF.ipynb>.

Thanks in advance for entertaining this request

Regards

Rodney

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