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MNE: Magnetoencephalography (MEG) and Electroencephalography (EEG) in Python
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Wavelet-ICA implementation? #11747

Open Hororohoruru opened 1 year ago

Hororohoruru commented 1 year ago

Describe the new feature or enhancement

Wavelet-ICA (wICA) as described in:

N.P. Castellanos, and V.A. Makarov (2006). 'Recovering EEG brain signals: Artifact suppression with wavelet enhanced independent component analysis' J. Neurosci. Methods, 158, 300--312.

Describe your proposed implementation

I imagine it could be included in mne.preprocessing, similar to ICA. I don't know how different it is from regular ICA for it to make sense to be a separate method or rather to be selected from ICA via parameters.

Describe possible alternatives

Instead of a separate class, it could be implemented as a new wavelet boolean parameter of the ICA class. I believe a separate method is clearer, but maybe the process of wICA with respect to regular ICA makes it easy to implement in the aforementioned way.

Additional context

No response

welcome[bot] commented 1 year ago

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agramfort commented 1 year ago

do you know a python implementation for this?

Hororohoruru commented 1 year ago

This is the only python implementation I found: https://github.com/compmem/ptsa/blob/master/ptsa/wica.py

agramfort commented 1 year ago

It’s gpl licensed so you cannot copy the code like this. Mne only accepts bsd or mit licenses

Hororohoruru commented 1 year ago

I understand. Is there any possibility of requesting it to be implemented in MNE in any other way?

agramfort commented 1 year ago

you can ask the authors if they accept to relicense in BSD

Message ID: @.***>

hoechenberger commented 1 year ago

If the implementation remains in that external package and MNE implements an interface, the licensing question goes away. You could Interface with it the same way as we currently use e.g. Picard. It can remain GPL in that case.

juangpc commented 1 year ago

Hi, maybe this can help. http://www.mat.ucm.es/~vmakarov/research.php

Not sure about licenses, but citing properly it will probably be ok, but perhaps you guys can ask him.

-- Juan

On Tue, Jun 27, 2023 at 5:44 PM Richard Höchenberger < @.***> wrote:

If the implementation remains in that external package and MNE implements an interface, the licensing question goes away. You could Interface with it the same way as we currently use e.g. Picard.

— Reply to this email directly, view it on GitHub https://github.com/mne-tools/mne-python/issues/11747#issuecomment-1610261274, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACEKMIA2CCDI4FVMO34WUBLXNNH3TANCNFSM6AAAAAAZPR4P3I . You are receiving this because you are subscribed to this thread.Message ID: @.***>

drammock commented 1 year ago

Not sure about licenses, but citing properly it will probably be ok

incorporating GPL-licensed code into a non-GPL-compatible codebase is not "probably OK". It is definitely a violation of the GPL license. If you want wICA added to MNE-Python, the options are:

  1. find an implementation (in Python or some other language) that has a compatible license (MIT, BSD...), and adapt/translate the code
  2. find an implementation with a non-compatible license and get permission from the author(s) to re-license the code as BSD, then adapt/translate
  3. re-implement the algorithm from first principles (i.e., looking at the equations in the published paper, but not looking at their code)
  4. what Richard said
juangpc commented 1 year ago

Not really following. The code is in matlab. It will need to get redeveloped at least. I already contacted the author. I do not want anything. Just trying to help, both the author, and mnepython.

On Wed, Jun 28, 2023 at 4:10 PM Daniel McCloy @.***> wrote:

Not sure about licenses, but citing properly it will probably be ok

incorporating GPL-licensed code into a non-GPL-compatible codebase is not "probably OK". It is definitely a violation of the GPL license. If you want wICA added to MNE-Python, the options are:

  1. find an implementation (in Python or some other language) that has a compatible license (MIT, BSD...), and adapt/translate the code
  2. find an implementation with a non-compatible license and get permission from the author(s) to re-license the code as BSD, then adapt/translate
  3. re-implement the algorithm from first principles (i.e., looking at the equations in the published paper, but not looking at their code)

— Reply to this email directly, view it on GitHub https://github.com/mne-tools/mne-python/issues/11747#issuecomment-1612036331, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACEKMIH63QVMSMNLU7VHN3DXNSFTPANCNFSM6AAAAAAZPR4P3I . You are receiving this because you commented.Message ID: @.***>

--

-- Juan

drammock commented 1 year ago

Not really following.

@juangpc what part was unclear?

The code is in matlab.

It does not matter what language the code is written in. If it is GPL licensed, we need permission from its author to re-license it in order to legally incorporate it into MNE-Python (which does not have a GPL-compatible license; MNE's license is more permissive than GPL). see https://www.gnu.org/licenses/gpl-faq.en.html#TranslateCode

It will need to get redeveloped at least.

that is why I said we would need to "adapt / translate the code".

juangpc commented 1 year ago

Hi, You're right, GPL code cannot be incorporated into a non-compatible license codebase. The link provided is from the authors' publication and contains code that is not GPL licensed. I was only trying to help find an example implementation since I know the authors. Sorry if it caused any confusion. Maybe the original creator of this issue can contact the authors and verify any potential issues.

-- Juan

On Wed, Jun 28, 2023 at 5:13 PM Daniel McCloy @.***> wrote:

Not really following.

@juangpc https://github.com/juangpc what part was unclear?

The code is in matlab.

It does not matter what language the code is written in. If it is GPL licensed, we need permission from its author to re-license it in order to legally incorporate it into MNE-Python (which does not have a GPL-compatible license; MNE's license is more permissive than GPL). see https://www.gnu.org/licenses/gpl-faq.en.html#TranslateCode

It will need to get redeveloped at least.

that is why I said we would need to "adapt / translate the code".

— Reply to this email directly, view it on GitHub https://github.com/mne-tools/mne-python/issues/11747#issuecomment-1612111914, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACEKMIHCDGGRQKEUNENWP7DXNSM7LANCNFSM6AAAAAAZPR4P3I . You are receiving this because you were mentioned.Message ID: @.***>

drammock commented 1 year ago

ah, OK, thanks for clarifying! I took a look at the .zip files containing the MATLAB code, and it appears that no license at all was specified, only a statement of "please acknowledge our work". In this case (because of the Berne Convention) we still must contact the author and get permission to translate their code and release it with a BSD-3 license --- when no license is specified, no re-use rights at all are transferred to us.

(see also https://softwareengineering.stackexchange.com/questions/207941/reusing-open-source-code-that-doesn-t-specify-a-license for discussion)

Hororohoruru commented 1 year ago

Hello all,

Thanks for the discussion and the suggestions. I will contact the original author about the Matlab implementation that Juan shared.

On Thu, 29 Jun 2023, 22:53 Daniel McCloy, @.***> wrote:

ah, OK, thanks for clarifying! I took a look at the .zip files containing the MATLAB code, and it appears that no license at all was specified, only a statement of "please acknowledge our work". In this case (because of the Berne Convention https://en.wikipedia.org/wiki/Berne_Convention) we still must contact the author and get permission to translate their code and release it with a BSD-3 license --- when no license is specified, no re-use rights at all are transferred to us.

— Reply to this email directly, view it on GitHub https://github.com/mne-tools/mne-python/issues/11747#issuecomment-1613223995, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIDOQVPJERLFPD2HQPLQCGDXNWCFDANCNFSM6AAAAAAZPR4P3I . You are receiving this because you authored the thread.Message ID: @.***>

Hororohoruru commented 1 year ago

Hello again,

The author just replied to me and he granted us permssion to adapt the code from his Matlab example to python and publish it on mne under a BSD-3 license.

agramfort commented 1 year ago

👌

sappelhoff commented 1 year ago

The author just replied to me and he granted us permssion to adapt the code from his Matlab example to python and publish it on mne under a BSD-3 license.

cool!

just for transparency it would be great to have this permission in this thread (preferably as a post directly be the author ... but maybe also a quoted email would be fine, if shared with permission)