Mailman 3 July 2014 - scikit-image

Make Pillow a requirement
by Juan Nunez-Iglesias July 11, 2014

July 11, 2014

@jjhelmus and I are having a discussion regarding IO and how tests fail if you don't have any of Pillow, PyQt, freeimage, etc, none of which are actually a requirement. As one of the sprint topics is fixing up IO, this would be a great thing to fix. Cheap solution: make Pillow a requirement. Expensive solution: write/pilfer our own IO modules, however inefficient they may be. (e.g. tifffile.py for tifs, maybe similar PNG) I don't see any *other* solution. Making mpl a requirement is not useful since their IO is also broken (e.g. images convert to float by default). Juan.

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Re: SciPy 2014 Tutorial and Sprints
by Juan Nunez-Iglesias July 10, 2014

July 10, 2014

Hi all! I've added a few items to Tony's list: ======= Add default structuring elements to morphology operations, and fall back on scipy.ndimage when parameters don't fit our optimized functions based on rank filters (2D images, bitdepth<12). Distribute tifffile.py with scikit-image and make it the default for TIFF files Other IO improvements, such as reordering plugin preferences, issuing warnings when certain plugins are used that rescale the image to float, etc. Improve 3D support (a few attendees requested this and expressed interest in helping with that) ======= Additionally, as I mentioned at the end of my talk and to all who would listen, I have no interest in locking myself in a basement for 8h while it's a nice day out. (You might recall that I was just as adamant 2 years ago, but back then I wasn't leading. =P) As such, I propose holding the skimage in one of: 201 (an official sprinting room) *only* if the shades are opened the tables outside of the Tejas dining room Gabriel's bar, either inside or outside. The last one is my preferred choice since we can also enjoy drinks while sprinting! Finally, depending on how things go, we may only sprint on skimage on Friday so that we can mingle with the other teams on Saturday. But we'll play this by ear. Juan. PS: Regarding the tutorials, I have been busy with my own talk and didn't have a chance to upload my solutions. Will do those now. PPS: I am also hereby proposing #skimage as the official hashtag of the scikit-image library. =) On Wed, Jul 9, 2014 at 10:59 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > Juan and I put together a tutorial for SciPy 2014. If anyone has 4 hours > to kill, here's a link to the first video, which should link to the other 3 > videos in the sidebar > > > http://www.youtube.com/watch?v=MP-MTiCETYg&list=PLYx7XA2nY5GfuhCvStxgbynFNr… > > The accompanying notebooks are here: > > https://github.com/scikit-image/skimage-tutorials/tree/master/scipy-2014 > > > Also, Juan and I are planning to hold a sprint on Friday. I know Steven > Sylvester and Thomas Caswell frequent this list (and are currently here for > the conference), so this is me putting you on the spot to get you to join > us for the sprint. Anyone else that reads this list should join in as well. > > I put together a list of possible sprint items on the wiki. Juan: I wrote > down what I remembered from our discussion; make sure you give it a look > over to make sure I didn't forget anything we talked about. Everyone: If > you have any ideas, now is the time to throw it out there: > > https://github.com/scikit-image/scikit-image/wiki/SciPy-2014-sprint-ideas > > By the way, a couple of the suggestions I wrote down might be > controversial, specifically, these two: > > > - Move and deprecate functions > - canny from filter to feature > - threshold_* from filter to exposure > > > Thoughts? > > -Tony > > -- > 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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SciPy 2014 Tutorial and Sprints
by Tony Yu July 9, 2014

July 9, 2014

Juan and I put together a tutorial for SciPy 2014. If anyone has 4 hours to kill, here's a link to the first video, which should link to the other 3 videos in the sidebar http://www.youtube.com/watch?v=MP-MTiCETYg&list=PLYx7XA2nY5GfuhCvStxgbynFNr… The accompanying notebooks are here: https://github.com/scikit-image/skimage-tutorials/tree/master/scipy-2014 Also, Juan and I are planning to hold a sprint on Friday. I know Steven Sylvester and Thomas Caswell frequent this list (and are currently here for the conference), so this is me putting you on the spot to get you to join us for the sprint. Anyone else that reads this list should join in as well. I put together a list of possible sprint items on the wiki. Juan: I wrote down what I remembered from our discussion; make sure you give it a look over to make sure I didn't forget anything we talked about. Everyone: If you have any ideas, now is the time to throw it out there: https://github.com/scikit-image/scikit-image/wiki/SciPy-2014-sprint-ideas By the way, a couple of the suggestions I wrote down might be controversial, specifically, these two: - Move and deprecate functions - canny from filter to feature - threshold_* from filter to exposure Thoughts? -Tony

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Re: [Numpy-discussion] Questions about fixes for 1.9.0rc2
by Nathaniel Smith July 4, 2014

July 4, 2014

On Fri, Jul 4, 2014 at 9:48 PM, Charles R Harris <charlesr.harris(a)gmail.com> wrote: > > On Fri, Jul 4, 2014 at 2:41 PM, Nathaniel Smith <njs(a)pobox.com> wrote: >> >> On Fri, Jul 4, 2014 at 9:33 PM, Charles R Harris >> <charlesr.harris(a)gmail.com> wrote: >> > >> > On Fri, Jul 4, 2014 at 2:09 PM, Nathaniel Smith <njs(a)pobox.com> wrote: >> >> >> >> On Fri, Jul 4, 2014 at 9:02 PM, Ralf Gommers <ralf.gommers(a)gmail.com> >> >> wrote: >> >> > >> >> > On Fri, Jul 4, 2014 at 10:00 PM, Charles R Harris >> >> > <charlesr.harris(a)gmail.com> wrote: >> >> >> >> >> >> On Fri, Jul 4, 2014 at 1:42 PM, Charles R Harris >> >> >> <charlesr.harris(a)gmail.com> wrote: >> >> >>> >> >> >>> Sebastian Seberg has fixed one class of test failures due to the >> >> >>> indexing >> >> >>> changes in numpy 1.9.0b1. There are some remaining errors, and in >> >> >>> the >> >> >>> case >> >> >>> of the Matplotlib failures, they look to me to be Matplotlib bugs. >> >> >>> The >> >> >>> 2-d >> >> >>> arrays that cause the error are returned by the overloaded >> >> >>> _interpolate_single_key function in CubicTriInterpolator that is >> >> >>> documented >> >> >>> in the base class to return a 1-d array, whereas the actual >> >> >>> dimensions >> >> >>> are >> >> >>> of the form (n, 1). The question is, what is the best work around >> >> >>> here >> >> >>> for >> >> >>> these sorts errors? Can we afford to break Matplotlib and other >> >> >>> packages on >> >> >>> account of a bug that was previously accepted by Numpy? >> >> > >> >> > >> >> > It depends how bad the break is, but in principle I'd say that >> >> > breaking >> >> > Matplotlib is not OK. >> >> >> >> I agree. If it's easy to hack around it and issue a warning for now, >> >> and doesn't have other negative consequences, then IMO we should give >> >> matplotlib a release or so worth of grace period to fix things. >> > >> > >> > Here is another example, from skimage. >> > >> > ====================================================================== >> > ERROR: test_join.test_relabel_sequential_offset1 >> > ---------------------------------------------------------------------- >> > Traceback (most recent call last): >> > File "X:\Python27-x64\lib\site-packages\nose\case.py", line 197, in >> > runTest >> > self.test(*self.arg) >> > File >> > >> > "X:\Python27-x64\lib\site-packages\skimage\segmentation\tests\test_join.py", >> > line 30, in test_relabel_sequential_offset1 >> > ar_relab, fw, inv = relabel_sequential(ar) >> > File >> > "X:\Python27-x64\lib\site-packages\skimage\segmentation\_join.py", >> > line 127, in relabel_sequential >> > forward_map[labels0] = np.arange(offset, offset + len(labels0) + 1) >> > ValueError: shape mismatch: value array of shape (6,) could not be >> > broadcast >> > to indexing result of shape (5,) >> > >> > Which is pretty clearly a coding error. Unfortunately, the error is in >> > the >> > package rather than the test. >> > >> > The only easy way to fix all of these sorts of things is to revert the >> > indexing changes, and I'm loathe to do that. Grrr... >> >> Ugh, that's pretty bad :-/. Do you really think we can't use a >> band-aid over the new indexing code, though? > > > Yeah, we can. But Sebastian doesn't have time and I'm unfamiliar with the > code, so it may take a while... Fair enough! I guess that if what are (arguably) bugs in matplotlib and scikit-image are holding up the numpy release, then it's worth CC'ing their mailing lists in case someone feels like volunteering to fix it... ;-). -n -- Nathaniel J. Smith Postdoctoral researcher - Informatics - University of Edinburgh http://vorpus.org

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Re: Doctest failures
by Juan Nunez-Iglesias July 3, 2014

July 3, 2014

Done: https://github.com/scikit-image/scikit-image/issues/1048 On Tue, Jul 1, 2014 at 7:14 PM, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: > On Tue, Jul 1, 2014 at 5:34 AM, Juan Nunez-Iglesias <jni.soma(a)gmail.com> > wrote: > > I did not, nor do I think I will until post-SciPy. (Or at the sprint > itself, > > really.) > > No problem--just file it for us somewhere, please. I will try to help > during the sprints where possible. > > Regards > 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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Re: Building skimage wheels for OS X using Travis CI
by Jonathan Helmus July 2, 2014

July 2, 2014

On 7/1/14, 3:13 PM, Stéfan van der Walt wrote: > Hi Jonathan > > On Tue, Jul 1, 2014 at 5:29 PM, Jonathan Helmus <jjhelmus(a)gmail.com> wrote: >> Next up, is to use AppVeyor [2] to build wheel files for Windows. I has >> able to get a wheel for Python 3.3 built [3] but Python 2.7 looked more >> difficult. > My attempt just to get a working test suite is here: > > https://github.com/stefanv/scikit-image/tree/appveyor > > If you have any ideas on how to fix that, I'd be happy to merge the PR > and have official Windows tests. > > Stéfan > I think I should be able to get the test suite running at least for Python 3.3/3.4 on AppVeyor. I'll look into it in detail during the sprints at the SciPy conference. - Jonathan Helmus

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Re: Building skimage wheels for OS X using Travis CI
by Stéfan van der Walt July 1, 2014

July 1, 2014

On Wed, Jul 2, 2014 at 12:29 AM, Matthew Brett <matthew.brett(a)gmail.com> wrote: >>> http://a365fff413fe338398b6-1c8a9b3114517dc5fe17b7c3f8c63a43.r19.cf2.rackcd… >> >> Is there a way to get a friendlier URL for this location? > > Do y'all have a cname you can use? Here we go: http://wheels.scikit-image.org/

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Re: Building skimage wheels for OS X using Travis CI
by Stéfan van der Walt July 1, 2014

July 1, 2014

Hi Matthew On Wed, Jul 2, 2014 at 12:29 AM, Matthew Brett <matthew.brett(a)gmail.com> wrote: > Do y'all have a cname you can use? I'll set this up quickly. > Here's a very simple bash script to do that... > > https://github.com/scikit-image/scikit-image-wheels/blob/master/check_uploa… Perfect! How does this look: https://github.com/scikit-image/scikit-image/pull/1046 Stéfan

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Re: Building skimage wheels for OS X using Travis CI
by Matthew Brett July 1, 2014

July 1, 2014

Hi, On Tue, Jul 1, 2014 at 9:21 PM, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: > Hi Matthew > > On Tue, Jul 1, 2014 at 5:13 PM, Matthew Brett <matthew.brett(a)gmail.com> wrote: >> The wheels should appear in this directory: >> >> http://a365fff413fe338398b6-1c8a9b3114517dc5fe17b7c3f8c63a43.r19.cf2.rackcd… > > Is there a way to get a friendlier URL for this location? Do y'all have a cname you can use? >> cd scikit-image >> git co v0.10.1 >> cd dist >> curl -O http://a365fff413fe338398b6-1c8a9b3114517dc5fe17b7c3f8c63a43.r19.cf2.rackcd… >> curl -O http://a365fff413fe338398b6-1c8a9b3114517dc5fe17b7c3f8c63a43.r19.cf2.rackcd… >> curl -O http://a365fff413fe338398b6-1c8a9b3114517dc5fe17b7c3f8c63a43.r19.cf2.rackcd… >> cd .. >> twine upload dist/*.whl > > A script that automatically does this would make the release manager's > life so much easier. Here's a very simple bash script to do that... https://github.com/scikit-image/scikit-image-wheels/blob/master/check_uploa… Cheers, Matthew

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Re: Building skimage wheels for OS X using Travis CI
by Stéfan van der Walt July 1, 2014

July 1, 2014

Hi Matthew On Tue, Jul 1, 2014 at 5:13 PM, Matthew Brett <matthew.brett(a)gmail.com> wrote: > The wheels should appear in this directory: > > http://a365fff413fe338398b6-1c8a9b3114517dc5fe17b7c3f8c63a43.r19.cf2.rackcd… Is there a way to get a friendlier URL for this location? > cd scikit-image > git co v0.10.1 > cd dist > curl -O http://a365fff413fe338398b6-1c8a9b3114517dc5fe17b7c3f8c63a43.r19.cf2.rackcd… > curl -O http://a365fff413fe338398b6-1c8a9b3114517dc5fe17b7c3f8c63a43.r19.cf2.rackcd… > curl -O http://a365fff413fe338398b6-1c8a9b3114517dc5fe17b7c3f8c63a43.r19.cf2.rackcd… > cd .. > twine upload dist/*.whl A script that automatically does this would make the release manager's life so much easier. Stéfan

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