[Mne_analysis] Mne_analysis Digest, Vol 150, Issue 40
balandongiv at gmail.com
balandongiv at gmail.com
Thu Jul 23 21:55:33 EDT 2020
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Dear Clemens, Larson, Phillip,
Thanks for the detail explanation, really appreciate it.
Just a suggestion, maybe part of the discussion can be incorporated
somewhere along with mne FAQ or equivalent. This might be helpful,
especially to those new in the field.
Rodney
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Today's Topics:
1. Re: Why does MNE resample method does not sample the data
point to point? (Eric Larson)
2. Re: Why does MNE resample method does not sample the data
point to point? (Brunner, Clemens (clemens.brunner at uni-graz.at))
3. Re: Why does MNE resample method does not sample the data
point to point? (Phillip Alday)
----------------------------------------------------------------------
Message: 1
Date: Thu, 23 Jul 2020 08:40:56 -0400
From: Eric Larson <larson.eric.d at gmail.com>
Subject: Re: [Mne_analysis] Why does MNE resample method does not
sample the data point to point?
To: Discussion and support forum for the users of MNE Software
<mne_analysis at nmr.mgh.harvard.edu>
Message-ID:
<CAGu2niVV+79nq5Yu17B4VzB3PS71x7sFTy8HKNukDxnaDdi6hQ at mail.gmail.com>
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>
> My understanding of downsampling is that it is an operation to
> decrease the sample rate of x by keeping the first sample and then
> every nth sample after the first.
>
Resampling typically consists of two steps: low-pass filtering to avoid
aliasing, then sample rate reduction (subselecting samples from the
resulting signal). The low-passing actually changes the values, so the
subselection-of-filtered-data step will not necessarily yield points that
were "on" the original signal.
> May I know whether this issue is due to the ringing artifacts or due
> to other problems?
>
In this case it's likely due to the (implicit) low-pass filtering in the
frequency-domain resampling of the signal. It looks pretty reasonable to me.
If you want to play around with it a bit, you can
1. Call scipy.signal.resample directly on your data and see how closely it
matches.
2. Pad your signal, call scipy.signal.resample, and remove the (now
reduced-length) padding -- this is what MNE does internally.
3. Use scipy.signal.resample_poly directly on your data.
4. Manually low-pass filter and then directly subselect samples from the
low-passed signal, which is what resample_poly does internally.
Hopefully these all give similar results for your signal(s).
Eric
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Message: 2
Date: Thu, 23 Jul 2020 12:57:29 +0000
From: "Brunner, Clemens (clemens.brunner at uni-graz.at)"
<clemens.brunner at uni-graz.at>
Subject: Re: [Mne_analysis] Why does MNE resample method does not
sample the data point to point?
To: Discussion and support forum for the users of MNE Software
<mne_analysis at nmr.mgh.harvard.edu>
Message-ID: <21199B34-7BD6-4C1B-81CC-749DFB86E3FC at uni-graz.at>
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Also note that the resample example
(https://docs.scipy.org/doc/scipy/reference/generated/scipy.signal.resample.
html) shows upsampling, i.e. the data has a lower sampling rate than the
resampled result. However, in the case of downsampling it is usually
necessary to avoid aliasing of frequencies above the resampled Nyquist
frequency. Therefore, the signal is typically low-pass filtered before the
resampling step. As Eric mentioned, this anti-aliasing filter is what
actually changes the signal values, but it is necessary to avoid aliasing
artifacts.
AFAIK, scipy.signal.resample doesn't include an anti-aliasing filter, but
both scipy.signal.resample_poly as well as scipy.signal.decimate apply such
a low-pass filter before resampling. That's also what MNE does.
Clemens
> On 23.07.2020, at 14:40, Eric Larson <larson.eric.d at gmail.com> wrote:
>
> External Email - Use Caution
>
>
> My understanding of downsampling is that it is an operation to decrease
the sample rate of x by keeping the first sample and then every nth sample
after the first.
>
> Resampling typically consists of two steps: low-pass filtering to avoid
aliasing, then sample rate reduction (subselecting samples from the
resulting signal). The low-passing actually changes the values, so the
subselection-of-filtered-data step will not necessarily yield points that
were "on" the original signal.
>
> May I know whether this issue is due to the ringing artifacts or due to
other problems?
>
> In this case it's likely due to the (implicit) low-pass filtering in
> the frequency-domain resampling of the signal. It looks pretty
> reasonable to me. If you want to play around with it a bit, you can
>
> 1. Call scipy.signal.resample directly on your data and see how closely it
matches.
> 2. Pad your signal, call scipy.signal.resample, and remove the (now
reduced-length) padding -- this is what MNE does internally.
> 3. Use scipy.signal.resample_poly directly on your data.
> 4. Manually low-pass filter and then directly subselect samples from the
low-passed signal, which is what resample_poly does internally.
>
> Hopefully these all give similar results for your signal(s).
>
> Eric
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
------------------------------
Message: 3
Date: Thu, 23 Jul 2020 15:09:44 +0200
From: Phillip Alday <phillip.alday at mpi.nl>
Subject: Re: [Mne_analysis] Why does MNE resample method does not
sample the data point to point?
To: Discussion and support forum for the users of MNE Software
<mne_analysis at nmr.mgh.harvard.edu>, "Brunner, Clemens
(clemens.brunner at uni-graz.at)" <clemens.brunner at uni-graz.at>
Message-ID: <16e39842-34bd-465d-9491-b5651302add4 at mpi.nl>
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I think the up- vs. downsampling distinction is also really important for
expectations here, as is the distinction between decimating and resampling
(I recall there was a thread about that a few years back with similar
confusion, if somebody wants to do the effort of searching for it)
Phillip
On 23/7/20 2:57 pm, Brunner, Clemens (clemens.brunner at uni-graz.at) wrote:
> External Email - Use Caution
>
> Also note that the resample example
(https://docs.scipy.org/doc/scipy/reference/generated/scipy.signal.resample.
html) shows upsampling, i.e. the data has a lower sampling rate than the
resampled result. However, in the case of downsampling it is usually
necessary to avoid aliasing of frequencies above the resampled Nyquist
frequency. Therefore, the signal is typically low-pass filtered before the
resampling step. As Eric mentioned, this anti-aliasing filter is what
actually changes the signal values, but it is necessary to avoid aliasing
artifacts.
>
> AFAIK, scipy.signal.resample doesn't include an anti-aliasing filter, but
both scipy.signal.resample_poly as well as scipy.signal.decimate apply such
a low-pass filter before resampling. That's also what MNE does.
>
> Clemens
>
>
>> On 23.07.2020, at 14:40, Eric Larson <larson.eric.d at gmail.com> wrote:
>>
>> External Email - Use Caution
>>
>>
>> My understanding of downsampling is that it is an operation to decrease
the sample rate of x by keeping the first sample and then every nth sample
after the first.
>>
>> Resampling typically consists of two steps: low-pass filtering to avoid
aliasing, then sample rate reduction (subselecting samples from the
resulting signal). The low-passing actually changes the values, so the
subselection-of-filtered-data step will not necessarily yield points that
were "on" the original signal.
>>
>> May I know whether this issue is due to the ringing artifacts or due to
other problems?
>>
>> In this case it's likely due to the (implicit) low-pass filtering in
>> the frequency-domain resampling of the signal. It looks pretty
>> reasonable to me. If you want to play around with it a bit, you can
>>
>> 1. Call scipy.signal.resample directly on your data and see how closely
it matches.
>> 2. Pad your signal, call scipy.signal.resample, and remove the (now
reduced-length) padding -- this is what MNE does internally.
>> 3. Use scipy.signal.resample_poly directly on your data.
>> 4. Manually low-pass filter and then directly subselect samples from the
low-passed signal, which is what resample_poly does internally.
>>
>> Hopefully these all give similar results for your signal(s).
>>
>> Eric
>>
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
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