Mailman 3 January 2013 - scikit-image

Policy for import of submodules
by Juan Nunez-Iglesias Jan. 30, 2013

Jan. 30, 2013

Hi, Does scikit-image have a specific policy for how imports should work? For example, as far as I know, numpy currently imports everything into the np namespace with: import numpy as np However, the following raises an error, even though the import statement works fine: import skimage as skim coins = skim.data.coins() giving the error: --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) <ipython-input-3-0ce27ef61295> in <module>() ----> 1 coins = skim.data.coins() AttributeError: 'module' object has no attribute 'data' But some things *are* in the top-level namespace. The following works fine: import skimage as skimfrom skimage import data coins = data.coins() coins = skim.img_as_float(coins) So my question is, is this behaviour by design, or should there be nothing at all in the top-level, or should everything be imported?

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Re: canvastools subpackage for scikit-image viewer
by Tony Yu Jan. 25, 2013

Jan. 25, 2013

On Thu, Dec 27, 2012 at 11:56 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > Hi Tony > > On Wed, Dec 26, 2012 at 10:41 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > > I just added another tool: A canvas painter. It's a bit less responsive > than > > I'd like, but I think it's as fast as it'll get (it's limited by > > matplotlib's blitting support for images). Check out the watershed demo > in > > the `viewer_examples/plugins` folder, which uses the paint tool to > generate > > markers for watershed segmentation. > > Finally, a path to that FFT filter painter I've had in mind! This is > very exciting. > > By the way, it took me a while to figure out to press "enter" to run > the segmentation, so how about printing some instructions to the > terminal? > > Thanks again, > Stéfan > > Sorry for the really late reply on this. Actually, the demo should have printed instructions to the terminal in that version. In any case, getting the user to press enter wasn't great for usability. I just changed this demo<https://github.com/tonysyu/scikit-image/commit/230fefa748db13af928e5cf69989…> so that you press a button to display the watershed segmentation. -T

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Re: Release plan for 0.8
by Schönberger Johannes Jan. 22, 2013

Jan. 22, 2013

Hi, some bugs have been fixed so far, thanks to everyone. This mail serves as a reminder for everyone who encountered any remaining problems with the current development version, since I plan to push out 0.8 in two days. Regards, Johannes

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Release plan for 0.8
by Johannes Schönberger Jan. 17, 2013

Jan. 17, 2013

Hi everybody, a lot of features have been added since we released version 0.7 about 4 months ago. I therefore suggest to make a feature freeze for the next week until January 23rd and only merge bugfixes in this time frame. Are there any changes you want to see in 0.8? It would be great if we could test the current development version on all common system environments to ensure we don't release a broken version. For me it works on OSX 10.8, Python 2.7 and Ubuntu 12.10 32bit, Python 2.7. Regards, Johannes

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Re: When will 0.8 official be released?
by Johannes Schönberger Jan. 15, 2013

Jan. 15, 2013

Hi Tony, OK, I'll give it a try! There is one small PR (https://github.com/scikit-image/scikit-image/pull/413) I would like to merge before I would set the timeline. I will get in touch with you if I encounter any problems. Regards, Johannes 2013/1/15 Tony Yu <tsyu80(a)gmail.com>: > On Wed, Jan 9, 2013 at 8:08 PM, Steven Silvester > <steven.silvester(a)gmail.com> wrote: >> >> Johannes, >> >> RELEASE.txt looks pretty well laid out. Perhaps you could cut a "release >> candidate", and wait until next month for the final release and the Debian >> version. >> >> Let me know if I can be of service. I maintain a PyPi package. >> >> >> Regards, >> Steve > > > > Sorry, I meant to respond sooner, but I've been busy. I think it's a great > idea to get an early start on the release. > > In particular, there's some grace period where we should announce a pending > release. Any bug fixes or *small* enhancements that people want to get in > before the release should be added at this time (~week). Then, there should > be another week or so for testing. (I don't think we've done release > branches in the past, but it might be a good idea.) > > So, to summarize, Johannes: I think it'd be great if you could get the ball > rolling by setting the timeline. You may want to take a look at my email > preparing for the 0.7 release. > > Also, as Steve suggests, RELEASE.txt is pretty thorough. The previous > release was the first release not handled by Stéfan, and I more or less > followed that document for the release. (Well, I probably also sent numerous > emails to Stéfan, too.) So if you're up for it, Johannes, it might be a good > idea to give it a go. (And any improvements you can make to RELEASE.txt > would be great.) > > Just a reminder: We may want to revisit the docs version linked on the > website after this release. > > Cheers, > -Tony > > -- > >

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Re: When will 0.8 official be released?
by Steven Silvester Jan. 15, 2013

Jan. 15, 2013

Johannes, RELEASE.txt looks pretty well laid out. Perhaps you could cut a "release candidate", and wait until next month for the final release and the Debian version. Let me know if I can be of service. I maintain a PyPi package. Regards, Steve

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Re: Master branch fails tests?
by Johannes Schönberger Jan. 10, 2013

Jan. 10, 2013

I think this is only necessary if new have been added or removed. Am Donnerstag, 10. Januar 2013 schrieb Juan Nunez-Iglesias : > That did the trick! Any guidelines on when I should do a full working tree > cleanup? Every build? > > On Thu, Jan 10, 2013 at 9:12 PM, Stéfan van der Walt <stefan(a)sun.ac.za<javascript:_e({}, 'cvml', 'stefan(a)sun.ac.za');> > > wrote: > >> Hi Juan >> >> On Thu, Jan 10, 2013 at 11:46 AM, Juan Nunez-Iglesias >> <jni.soma(a)gmail.com <javascript:_e({}, 'cvml', 'jni.soma(a)gmail.com');>> >> wrote: >> > Am I doing something wrong? I can't get master to work on OSX; 6 tests >> fail >> > with the following import error: >> >> Could you try: >> >> git checkout master >> git reset --hard origin/master >> git clean -xdf >> make >> >> And then try again? The tests run fine over here. >> >> Thanks! >> Stéfan >> >> -- >> >> >> > -- > > >

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Re: Master branch fails tests?
by Juan Nunez-Iglesias Jan. 10, 2013

Jan. 10, 2013

That did the trick! Any guidelines on when I should do a full working tree cleanup? Every build? On Thu, Jan 10, 2013 at 9:12 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > Hi Juan > > On Thu, Jan 10, 2013 at 11:46 AM, Juan Nunez-Iglesias > <jni.soma(a)gmail.com> wrote: > > Am I doing something wrong? I can't get master to work on OSX; 6 tests > fail > > with the following import error: > > Could you try: > > git checkout master > git reset --hard origin/master > git clean -xdf > make > > And then try again? The tests run fine over here. > > Thanks! > Stéfan > > -- > > >

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Re: Master branch fails tests?
by Stéfan van der Walt Jan. 10, 2013

Jan. 10, 2013

Hi Juan On Thu, Jan 10, 2013 at 11:46 AM, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: > Am I doing something wrong? I can't get master to work on OSX; 6 tests fail > with the following import error: Could you try: git checkout master git reset --hard origin/master git clean -xdf make And then try again? The tests run fine over here. Thanks! Stéfan

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Master branch fails tests?
by Juan Nunez-Iglesias Jan. 10, 2013

Jan. 10, 2013

Hi everyone, Am I doing something wrong? I can't get master to work on OSX; 6 tests fail with the following import error: ====================================================================== ERROR: Failure: ImportError (cannot import name denoise_tv_chambolle) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/loader.py", line 390, in loadTestsFromName addr.filename, addr.module) File "/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/Volumes/Projects/skimage/skimage/feature/__init__.py", line 4, in <module> from .peak import peak_local_max File "/Volumes/Projects/skimage/skimage/feature/peak.py", line 3, in <module> from ..filter import rank_order File "/Volumes/Projects/skimage/skimage/filter/__init__.py", line 6, in <module> from ._denoise import denoise_tv_chambolle, tv_denoise ImportError: cannot import name denoise_tv_chambolle This is after running make all. If I do `git co ec3f3`, i.e. before implementation of `tv_denoise`, it runs fine. nuneziglesiasj@jni-lscc-mbp Thu Jan 10 15:45 ~/projects/skimage ((no branch))$ make test nosetests skimage Exception AttributeError: "'UmfpackContext' object has no attribute '_symbolic'" in <bound method UmfpackContext.__del__ of <scipy.sparse.linalg.dsolve.umfpack.umfpack.UmfpackContext object at 0x108caddd0>> ignored ...........................................................................................................................................................................................................................................................SSSSS.....SSSS.....................S......................SSS.....................................................S....................................................................................................................................................................................................... ---------------------------------------------------------------------- Ran 565 tests in 22.690s OK (SKIP=14) Any ideas?

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