Mailman 3 May 2014 - scikit-image

I/O infrastructure
by Stéfan van der Walt 15 May '14

15 May '14

Hi all, Juan recently again brought to my attention the dismal state of the scikit-image I/O infrastructure. This needs to be fixed for 0.11 (0.10 is almost out the door--this weekend, I hope!). We are currently relying on other libraries to do the job, and while it allows you to do "from skimage import io; io.imread(anything)" on almost any platform, it's just not working--we need reproducible backends. My current thinking is thus: make Luis's "imread" [0] a dependency, and remove all plugins from scikit-image. Users can, of course, still load data using mpl, imread, astropy or whatever suits them. In the documentation, we may provide recipes for handling files like ITK, gdal etc. if that proves useful. What do you think? Stéfan [0] https://github.com/luispedro/imread

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Broken PR display
by Stéfan van der Walt 13 May '14

13 May '14

Hi everyone An update from GitHub on the PR from Abid Rahman that was closed from their side without actually being integrated into scikit-image. The dangers of rebase :) Cheers Stéfan ---------- Forwarded message ---------- From: Brian Levine (GitHub Staff) Date: Wed, May 14, 2014 at 1:36 AM Subject: Re: Broken PR display To: Stefan van der Walt Hey Stefan It looks like the head branch of that pull request was updated to include a list of commits that already existed in master. When the head branch of a pull request is changed, the commit list is updated to reflect the diff between it and the base branch at that time. In this case, the commits pushed to the head branch existed in the upstream base branch, so the pull request was closed and marked as merged. I hope this helps explain things a bit. Let us know if you have any other questions. Brian GitHub Support > This PR claims that it has been merged, which it has not. Clicking on the the merged commit id at the bottom takes me to work done in an entirely different PR.

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Re: Potential contribution: subpixel cross correlation
by Stéfan van der Walt 13 May '14

13 May '14

Hi Michael On Tue, May 13, 2014 at 6:02 AM, Michael Sarahan <msarahan(a)gmail.com> wrote: > I wrote to Prof. Fienup last Tuesday, but haven't heard back. The work is > published, and to the best of my knowledge unpatented (Google patent search > turns up nothing.) Let me know if you'd still be up for a PR. I would prefer to get Prof. Fienup's approval of the work. However, if that cannot be obtained we can still publish code if we can show that it was derived purely from the published information (not from the "tainted" code the current version is based on). Regards Stéfan

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Re: Potential contribution: subpixel cross correlation
by Michael Sarahan 13 May '14

13 May '14

Hi Stefan, I wrote to Prof. Fienup last Tuesday, but haven't heard back. The work is published, and to the best of my knowledge unpatented (Google patent search turns up nothing.) Let me know if you'd still be up for a PR. Best, Michael On Mon, May 5, 2014 at 3:00 AM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > Hi Michael > > On Mon, May 5, 2014 at 5:21 AM, Michael Sarahan <msarahan(a)gmail.com> > wrote: > > Sorry guys, things aren't looking good for the license. Manuel was kind > > enough to reply to me and to forward my message to James Fienup, but it > > seems the license (or lack thereof) was already a point of contention > > between Manuel and James. > > Did James sound like he was willing to negotiate on the license terms? > If not, is this work published and unpatented? > > Stéfan > > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/d/optout. >

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0.10
by Johannes Schönberger 08 May '14

08 May '14

Hi everyone, I think, we are finally close to release 0.10. Does anyone have any outstanding issues? Otherwise I could arrange some time to finish up the release (which would also be good for the paper, as we can then refer to version 0.10). Johannes

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Re: Help with Windows buildbot errors
by Johannes Schönberger 06 May '14

06 May '14

I am not sure, where I read it, but I think the pillow plugin in conda is broken on Windows. On May 6, 2014, at 11:31 AM, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: > Hi, everyone > > Continuous integration for Windows is almost ready, but the test suite > is failing: > > https://ci.appveyor.com/project/stefanv/scikit-image-494/build/1.0.39 > > Has anyone seen those errors before, and do you have suggestions on > how to fix them? > > Thanks > Stéfan > > -- > You received this message because you are subscribed to the Google Groups "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/d/optout.

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Help with Windows buildbot errors
by Stéfan van der Walt 06 May '14

06 May '14

Hi, everyone Continuous integration for Windows is almost ready, but the test suite is failing: https://ci.appveyor.com/project/stefanv/scikit-image-494/build/1.0.39 Has anyone seen those errors before, and do you have suggestions on how to fix them? Thanks Stéfan

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Re: SciPy 2014, revisited
by Stéfan van der Walt 05 May '14

05 May '14

On Sat, May 3, 2014 at 5:26 AM, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: > So, both my and Tony's scikit-image tutorial and my talk have been accepted > to SciPy 2014, so it is confirmed that I will be there! Anyone else? Would > be great to have a significant skimage contingent there! Thanks for giving us such a strong presence at the conference! Unfortunately, I won't be at the conference this year, but I will be supporting enthusiastically from the side. Stéfan

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Re: Potential contribution: subpixel cross correlation
by Stéfan van der Walt 05 May '14

05 May '14

Hi Michael On Mon, May 5, 2014 at 5:21 AM, Michael Sarahan <msarahan(a)gmail.com> wrote: > Sorry guys, things aren't looking good for the license. Manuel was kind > enough to reply to me and to forward my message to James Fienup, but it > seems the license (or lack thereof) was already a point of contention > between Manuel and James. Did James sound like he was willing to negotiate on the license terms? If not, is this work published and unpatented? Stéfan

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Re: Potential contribution: subpixel cross correlation
by Michael Sarahan 05 May '14

05 May '14

Sorry guys, things aren't looking good for the license. Manuel was kind enough to reply to me and to forward my message to James Fienup, but it seems the license (or lack thereof) was already a point of contention between Manuel and James. I'm going to leave my branch open for anyone wanting to use the code, but I think it's better to not include officially until a license is determined for the parent work. https://github.com/msarahan/scikit-image/tree/PhaseCorrelation Best, Michael On Mon, Apr 28, 2014 at 8:49 PM, Juan Nunez-Iglesias <jni.soma(a)gmail.com>wrote: > On Sun, Apr 27, 2014 at 10:53 AM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: >> >> Perhaps Juan can answer this one--he is our most vocal 3D proponent! >> > > Haha, 3D is not the same as 2D+c! I'm actually also used to grayscale EM > images, but in 3D. For that case, I think the generalisation would be > straightforward. For 2D+c, I have no idea! > > In the meanwhile, getting a version up and running with tests in 2D is >> a great start. >> > > Or 3D grayscale. Just a suggestion. ;) > > Juan. > > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/d/optout. >

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