Mailman 3 November 2017 - scikit-image

Re: [scikit-image] linking to GPL code from BSD code (was: BM3D)
by Josh Warner 02 Nov '17

02 Nov '17

I'm not a lawyer, but I believe there is a longstanding misunderstanding on this matter and the FSF is in the wrong. The FSF, in the GPL FAQ, says that maintained dynamic linking, as exhibited in Python, infects any package that imports. However, to trigger this clause the 'linked' package must constitute a derivative work, which has a definite legal meaning. The FSF's justification in the case of static linking is relatively sound. However, legal rulings on the matter of dynamic linking, as in Python (*Galoob v. Nintendo*) disagree. For those interested, the actual ruling for *Galoob v. Nintendo*: https://law.justia.com/cases/federal/appellate-courts/F2/964/965/341457/ The relevant portion of the ruling, which stands today and was affirmed in *Micro Star v. FormGen Inc.*, states rather concretely A derivative work must incorporate a protected work in some concrete or > permanent "form." > > Ergo, despite what the FSF states, *on the basis of current law dynamic linking - linking without creating a file in any way, simply asking another library to do something - does not constitute creation of a derivative work, and thus does not infringe the GPL.* Linking as a matter of current law involves actually combining the linked code with the code from the linking package into a concrete form, generally a file, which can then be executed. Thus, static linking infects, but dynamic linking does not. Again, *this isn't what the FSF says, but ultimately the GPL means what it actually says, not what the FSF wants it to. *Consider this the same way that the US Constitution exists separately from the Federalist papers and other writings of the founding fathers. Despite this being relatively clearly settled law, very few people call the FSF out on it, and fewer have the guts to act appropriately as permitted under the law. Most It's actually harming communities, though, and PyFFTW is a great example. If anyone can actually refute this, I'm all ears. On Wed, Nov 1, 2017 at 6:43 PM, Nathaniel Smith <njs(a)pobox.com> wrote: > On Wed, Nov 1, 2017 at 6:22 PM, Juan Nunez-Iglesias <jni.soma(a)gmail.com> > wrote: > > On Thu, Nov 2, 2017 at 12:14 PM, Stefan van der Walt < > stefanv(a)berkeley.edu> > > wrote: > >> > >> On Wed, Nov 1, 2017, at 16:32, Juan Nunez-Iglesias wrote: > >> > Stéfan, as an aside, I notice that SPORCO is BSD, but uses PyFFTW. > >> > >> Yes, I'm aware. If we ever do rely on this code, we'll have to switch > >> that out. > > > > > > I'm not pointing it out to switch it out. Rather, I've heard from many > GPL > > proponents that linking/importing GPL in BSD code is fine, and saying the > > opposite is simply FUD. So I'm wondering whether SPORCO is unwittingly > > illegal or simply bearing this out. Know of any cases where this has been > > specifically tested? > > You can combine GPL and BSD code, and it's certainly not illegal; it's > just that you may have to treat the combined work as being under the > GPL. > > -n > > -- > Nathaniel J. Smith -- https://vorpus.org > _______________________________________________ > scikit-image mailing list > scikit-image(a)python.org > https://mail.python.org/mailman/listinfo/scikit-image >

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Re: [scikit-image] linking to GPL code from BSD code (was: BM3D)
by Stefan van der Walt 02 Nov '17

02 Nov '17

On Wed, Nov 1, 2017, at 18:43, Nathaniel Smith wrote: > > I'm not pointing it out to switch it out. Rather, I've heard from many GPL > > proponents that linking/importing GPL in BSD code is fine, and saying the > > opposite is simply FUD. So I'm wondering whether SPORCO is unwittingly > > illegal or simply bearing this out. Know of any cases where this has been > > specifically tested? > > You can combine GPL and BSD code, and it's certainly not illegal; it's > just that you may have to treat the combined work as being under the > GPL. And advertise it as such; whereas scikit-image explicitly labels itself as BSD. In a sense, not too dissimilar from packages released under BSD, but then implement patented algorithms. You have to make your users aware of what they're getting themselves into. Stéfan

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Re: [scikit-image] linking to GPL code from BSD code (was: BM3D)
by Nathaniel Smith 02 Nov '17

02 Nov '17

On Wed, Nov 1, 2017 at 6:22 PM, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: > On Thu, Nov 2, 2017 at 12:14 PM, Stefan van der Walt <stefanv(a)berkeley.edu> > wrote: >> >> On Wed, Nov 1, 2017, at 16:32, Juan Nunez-Iglesias wrote: >> > Stéfan, as an aside, I notice that SPORCO is BSD, but uses PyFFTW. >> >> Yes, I'm aware. If we ever do rely on this code, we'll have to switch >> that out. > > > I'm not pointing it out to switch it out. Rather, I've heard from many GPL > proponents that linking/importing GPL in BSD code is fine, and saying the > opposite is simply FUD. So I'm wondering whether SPORCO is unwittingly > illegal or simply bearing this out. Know of any cases where this has been > specifically tested? You can combine GPL and BSD code, and it's certainly not illegal; it's just that you may have to treat the combined work as being under the GPL. -n -- Nathaniel J. Smith -- https://vorpus.org

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linking to GPL code from BSD code (was: BM3D)
by Juan Nunez-Iglesias 02 Nov '17

02 Nov '17

On Thu, Nov 2, 2017 at 12:14 PM, Stefan van der Walt <stefanv(a)berkeley.edu> wrote: > On Wed, Nov 1, 2017, at 16:32, Juan Nunez-Iglesias wrote: > > Stéfan, as an aside, I notice that SPORCO is BSD, but uses PyFFTW. 🤔 > > Yes, I'm aware. If we ever do rely on this code, we'll have to switch > that out. > I'm not pointing it out to switch it out. Rather, I've heard from many GPL proponents that linking/importing GPL in BSD code is fine, and saying the opposite is simply FUD. So I'm wondering whether SPORCO is unwittingly illegal or simply bearing this out. Know of any cases where this has been specifically tested?

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Re: [scikit-image] BM3D denoising
by Juan Nunez-Iglesias 02 Nov '17

02 Nov '17

Thanks for the description, Greg! Very informative. I would hope that we could do BM(n+1)D in scikit-image… ;) Stéfan, as an aside, I notice that SPORCO is BSD, but uses PyFFTW. 🤔

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Re: [scikit-image] BM3D denoising
by Stefan van der Walt 01 Nov '17

01 Nov '17

On Wed, Nov 1, 2017, at 10:10, Gregory Lee wrote: > Juan: Similar to non-local means, BM3D looks at the similarity > between all patches in a local neighborhood. However rather than > simply computing weights based on the patch difference, similar 2D > patches are grouped into a 3D stack of patches (thus the 3D in BM3D). > This stack of similar patches is transformed with a sparsifying > transform, the coefficients are thresholded, the transforms is > inverted and then finally there is aggregation of the denoised > patches. This leads to substantial improvement over non-local means. I chatted to the author of SPORCO at SciPy---it looks like a great package, and may be useful here: http://bwohlberg.github.io/sporco/ Stéfan

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Re: [scikit-image] BM3D denoising
by Gregory Lee 01 Nov '17

01 Nov '17

Hi Srinivas, I am familiar with the BM3D algorithm and think it would be a good fit. As far as location, the code would fit best under the restoration subfolder where there are already routines for 2D and 3D non-local means. It is not likely to be trivial to implement because it will likely need some C/Cython code to have reasonable performance, but some code for neighborhood comparisons could be reused from the existing non-local means implementation. Please see the comments below on licensing terms (existing implementations I know of are not compatibly licensed so this means it would be need to be reimplemented from a description in the journal articles). Juan: Similar to non-local means, BM3D looks at the similarity between all patches in a local neighborhood. However rather than simply computing weights based on the patch difference, similar 2D patches are grouped into a 3D stack of patches (thus the 3D in BM3D). This stack of similar patches is transformed with a sparsifying transform, the coefficients are thresholded, the transforms is inverted and then finally there is aggregation of the denoised patches. This leads to substantial improvement over non-local means. The IPOL journal has an open source 2D implementation in C++, but it is under an incompatible LGPLv3 license so it could not be used as the basis for an implementation in scikit-image. http://www.ipol.im/pub/art/2012/l-bm3d/ If you just need something for immediate use, there is also a Cython-based wrapper for the IPOL BM3D code here: https://github.com/ericmjonas/pybm3d There is also a reference implementation from the original authors in Matlab + compiled MEX (no C/C++ source code to the MEX files is provided) http://www.cs.tut.fi/~foi/GCF-BM3D/ The IPOL paper provides a detailed overview that could be used as the basis for making a clean implementation. - Greg On Wed, Nov 1, 2017 at 12:25 PM, Srinivas V <srinivasv147(a)gmail.com> wrote: > > > On Wed, Nov 1, 2017 at 9:30 PM, <scikit-image-request(a)python.org> wrote: > >> Send scikit-image mailing list submissions to >> scikit-image(a)python.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://mail.python.org/mailman/listinfo/scikit-image >> or, via email, send a message with subject or body 'help' to >> scikit-image-request(a)python.org >> >> You can reach the person managing the list at >> scikit-image-owner(a)python.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of scikit-image digest..." >> >> >> Today's Topics: >> >> 1. New Contributor (Srinivas V) >> 2. Re: New Contributor (Juan Nunez-Iglesias) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Wed, 1 Nov 2017 19:37:56 +0530 >> From: Srinivas V <srinivasv147(a)gmail.com> >> To: scikit-image(a)python.org >> Subject: [scikit-image] New Contributor >> Message-ID: >> <CABXwt0+37gx=Ay2XGOEvsyx+nGOJtfxx-=K9aqrCtWg9VeGJ_w@mail. >> gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi, >> I am Srinivas I wish to contribute to this project. I am interested in >> implementing the BM3D denoising. Can someone please guide me through the >> process of getting started with the existing code base. >> Regards, >> V Srinivas >>

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BM3D denoising
by Srinivas V 01 Nov '17

01 Nov '17

On Wed, Nov 1, 2017 at 9:30 PM, <scikit-image-request(a)python.org> wrote: > Send scikit-image mailing list submissions to > scikit-image(a)python.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.python.org/mailman/listinfo/scikit-image > or, via email, send a message with subject or body 'help' to > scikit-image-request(a)python.org > > You can reach the person managing the list at > scikit-image-owner(a)python.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of scikit-image digest..." > > > Today's Topics: > > 1. New Contributor (Srinivas V) > 2. Re: New Contributor (Juan Nunez-Iglesias) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 1 Nov 2017 19:37:56 +0530 > From: Srinivas V <srinivasv147(a)gmail.com> > To: scikit-image(a)python.org > Subject: [scikit-image] New Contributor > Message-ID: > <CABXwt0+37gx=Ay2XGOEvsyx+nGOJtfxx-=K9aqrCtWg9VeGJ_w@ > mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi, > I am Srinivas I wish to contribute to this project. I am interested in > implementing the BM3D denoising. Can someone please guide me through the > process of getting started with the existing code base. > Regards, > V Srinivas >

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Re: [scikit-image] New Contributor
by Juan Nunez-Iglesias 01 Nov '17

01 Nov '17

Hi Srinivas, Thanks for reaching out on the mailing list. It’s the right first step. =) As a second step, please read our contributing document: http://scikit-image.org/docs/0.13.x/contribute.html Can you send us a reference to the algorithm you’re proposing? I have never heard of it… Thanks, Juan. On 2 Nov 2017, 1:08 AM +1100, Srinivas V <srinivasv147(a)gmail.com>, wrote: > Hi, > I am Srinivas I wish to contribute to this project. I am interested in implementing the BM3D denoising. Can someone please guide me through the process of getting started with the existing code base. > Regards, > V Srinivas > _______________________________________________ > scikit-image mailing list > scikit-image(a)python.org > https://mail.python.org/mailman/listinfo/scikit-image

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New Contributor
by Srinivas V 01 Nov '17

01 Nov '17

Hi, I am Srinivas I wish to contribute to this project. I am interested in implementing the BM3D denoising. Can someone please guide me through the process of getting started with the existing code base. Regards, V Srinivas

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