Mailman 3 October 2011 - scikit-image

Re: Math functions for uint8
by Stéfan van der Walt Oct. 18, 2011

Oct. 18, 2011

On Sun, Oct 16, 2011 at 10:31 AM, Tony Yu <tsyu80(a)gmail.com> wrote: > This may be a little low-level for skimage, but I just published a branch > with some math operations on uint8 arrays. > > https://github.com/tonysyu/scikits.image/compare/master...uint8_math Ideally, we do not want to do manipulations that overflow or underflow (and that probably means avoiding uint8 arithmetic). It is used in colormixer, because those values are for display purposes only. However, let's keep this code around for a while; now that it's been written, we can easily pull it in if it happens to solve a problem. Cheers Stéfan

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Re: Renaming scikits.image to skimage
by Stéfan van der Walt Oct. 18, 2011

Oct. 18, 2011

On Sun, Oct 16, 2011 at 10:31 PM, <bdholt1(a)gmail.com> wrote: > My 2c: I think the package name should move to skimage (as decided), and the repo name should be "scikits-image" I.e. > > https://github.com/scikits-image/scikits-image That seems reasonable. Then the downloaded zip files will be scikits-image-xx.zip, which contains the skimage package. Cheers Stéfan

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Re: Renaming scikits.image to skimage
by bdholt1＠gmail.com Oct. 17, 2011

Oct. 17, 2011

My 2c: I think the package name should move to skimage (as decided), and the repo name should be "scikits-image" I.e. https://github.com/scikits-image/scikits-image -----Original Message----- From: Stéfan van der Walt <stefan(a)sun.ac.za> Sender: scikits-image(a)googlegroups.com Date: Sun, 16 Oct 2011 22:28:04 To: <scikits-image(a)googlegroups.com> Reply-To: scikits-image(a)googlegroups.com Subject: Re: Renaming scikits.image to skimage On Sun, Oct 16, 2011 at 1:24 PM, Emmanuelle Gouillart <emmanuelle.gouillart(a)nsup.org> wrote: > I think we should move "everything" to skimage, except the name of the > source repo, and the name of the mailing list. A few examples of changes > that could be made (from a 'git grep scikits.image' in Nelle's skimage > branch) When you say source repo, do you agree that the url for the repo should be https://github.com/scikits-image/skimage ? Stéfan

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Re: Renaming scikits.image to skimage
by Emmanuelle Gouillart Oct. 16, 2011

Oct. 16, 2011

On Sun, Oct 16, 2011 at 12:55:58PM -0700, StÃ¯Â¿Â½fan van der Walt wrote: > On Sun, Oct 16, 2011 at 12:38 AM, Nelle Varoquaux > <nelle.varoquaux(a)gmail.com> wrote: > > I think scikit-learn decision was to still do the branding with the name > > "scikits-learn". In that case, I don't think it is necessary to rename the > > repository. > > What do you think about it ? > > If we rename the repository, there's a bit more work to do. > We're going to keep the scikits-image organisation on GitHub, but I > think we need to move the source repo to skimage.git (instead of > scikits.image.git). +1 I think we should move "everything" to skimage, except the name of the source repo, and the name of the mailing list. A few examples of changes that could be made (from a 'git grep scikits.image' in Nelle's skimage branch) TASKS.txt:Developing Open Source is great fun! Join us on the `scikits-image mailing-list doc/source/conf.py:copyright = u'2011, scikits-image team' doc/Makefile: --project-url=http://scikits-image.org \ (now that StÃ¯Â¿Â½fan kindly provided the new domain name!) ... and many similar occurrences found by git grep In some places, we could also use "the Image Scikit", to make clear that our package is... an image scikit. What do you think? Emmanuelle

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Re: Renaming scikits.image to skimage
by Stéfan van der Walt Oct. 16, 2011

Oct. 16, 2011

On Sun, Oct 16, 2011 at 12:38 AM, Nelle Varoquaux <nelle.varoquaux(a)gmail.com> wrote: > I think scikit-learn decision was to still do the branding with the name > "scikits-learn". In that case, I don't think it is necessary to rename the > repository. > What do you think about it ? > If we rename the repository, there's a bit more work to do. We're going to keep the scikits-image organisation on GitHub, but I think we need to move the source repo to skimage.git (instead of scikits.image.git). Stéfan

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Math functions for uint8
by Tony Yu Oct. 16, 2011

Oct. 16, 2011

This may be a little low-level for skimage, but I just published a branch with some math operations on uint8 arrays. https://github.com/tonysyu/scikits.image/compare/master...uint8_math Basically, it defines add/subtract/multiply/divide for uint8 arrays, but clips values instead of allowing values to overflow/underflow. I originally wrote them because I thought they were necessary to fix the underflow problems in morphological tophat, but it turned out that the underlying issue was different. Even so, they could be useful elsewhere: For example, I remember the Sobel filters had issues with underflow or overflow (I think the functions now cast to float). I noticed that there were some similar operations written in Cython (scikits/image/io/_plugins/_colormixer.pyx), but these look specific to the application (but are probably faster, too). Any thoughts would be appreciated, -Tony

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Re: Renaming scikits.image to skimage
by Nelle Varoquaux Oct. 16, 2011

Oct. 16, 2011

Hi Stéfan, 2011/10/15 Stéfan van der Walt <stefan(a)sun.ac.za> > Hi Nelle > > On Sat, Oct 15, 2011 at 9:21 AM, Nelle Varoquaux > <nelle.varoquaux(a)gmail.com> wrote: > > I've worked on renaming scikits.image to skimage. Unfortunately, I have > one > > Thanks for your hard work; this looks great. > > Do you think we should rename the entire repo as well? I.e. > > github.com/scikits-image/skimage.git > > ? > I think scikit-learn decision was to still do the branding with the name "scikits-learn". In that case, I don't think it is necessary to rename the repository. What do you think about it ? If we rename the repository, there's a bit more work to do. Nelle > > Regards > Stéfan >

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Re: Renaming scikits.image to skimage
by Nelle Varoquaux Oct. 16, 2011

Oct. 16, 2011

On 15 October 2011 22:17, Tony Yu <tsyu80(a)gmail.com> wrote: > > > On Sat, Oct 15, 2011 at 12:21 PM, Nelle Varoquaux < > nelle.varoquaux(a)gmail.com> wrote: > >> Hi all, >> >> I've worked on renaming scikits.image to skimage. Unfortunately, I have >> one test failing. I have no clue how to fix that, and would appreciate some >> help on that. >> You can have a look at the patch at : >> https://github.com/NelleV/scikits.image/compare/master...skimage >> >> I'm using numpy 1.6.1 and cython 0.15.1 >> >> ====================================================================== >> ERROR: test_project.test_homography >> ---------------------------------------------------------------------- >> Traceback (most recent call last): >> File >> "/home/nelle/Projets/skimage/env/lib/python2.6/site-packages/nose-1.1.2-py2.6.egg/nose/case.py", >> line 197, in runTest >> self.test(*self.arg) >> File >> "/home/nelle/Projets/skimage/skimage/transform/tests/test_project.py", line >> 23, in test_homography >> x90 = homography(x, M, order=1) >> File "/home/nelle/Projets/skimage/skimage/transform/project.py", line >> 101, in homography >> mode=mode, order=order, cval=cval) >> File >> "/home/nelle/Projets/skimage/env/lib/python2.6/site-packages/scipy-0.9.0-py2.6-linux-i686.egg/scipy/ndimage/interpolation.py", >> line 298, in map_coordinates >> output, order, mode, cval, None, None) >> RuntimeError: data type not supported >> >> Thanks, >> Nelle >> >> Hi Nelle, > > Thanks for working on this. I actually don't have any test failures when I > check out your branch. Nose reports 227 tests run (4 skips, but the skips > are b/c I don't have pyfits on my machine). > > I'm running cython 14.1 and numpy dev (and scipy dev), so my system isn't > exactly a match. But I can't imagine how these differences could change the > test behavior before and after the renaming. Are you sure the test passed > before the rename? > I still have this installation problem, really annoying with the cython compiled files, so I have ran the tests on master. I'll try to do that now. > > Also, if anyone else wants to test this branch, just note that git acts a > little weird with it. When I checkout the skimage branch, it adds the > skimage tree, but doesn't remove the scikits.image tree (which can cause > build/test problems). Similarly, switching back adds the scikits.image tree, > but doesn't remove the skimage tree. You'll need to manually remove these > before building/testing. > Git does not remove folders if there are unchecked files in them (*.pyc, *.so etc. Once we do the merge, it should be easier. > > Best, > -Tony >

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Re: Renaming scikits.image to skimage
by Stéfan van der Walt Oct. 15, 2011

Oct. 15, 2011

Hi Nelle On Sat, Oct 15, 2011 at 9:21 AM, Nelle Varoquaux <nelle.varoquaux(a)gmail.com> wrote: > I've worked on renaming scikits.image to skimage. Unfortunately, I have one Thanks for your hard work; this looks great. Do you think we should rename the entire repo as well? I.e. github.com/scikits-image/skimage.git ? Regards Stéfan

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Re: Renaming scikits.image to skimage
by Tony Yu Oct. 15, 2011

Oct. 15, 2011

On Sat, Oct 15, 2011 at 12:21 PM, Nelle Varoquaux <nelle.varoquaux(a)gmail.com > wrote: > Hi all, > > I've worked on renaming scikits.image to skimage. Unfortunately, I have one > test failing. I have no clue how to fix that, and would appreciate some help > on that. > You can have a look at the patch at : > https://github.com/NelleV/scikits.image/compare/master...skimage > > I'm using numpy 1.6.1 and cython 0.15.1 > > ====================================================================== > ERROR: test_project.test_homography > ---------------------------------------------------------------------- > Traceback (most recent call last): > File > "/home/nelle/Projets/skimage/env/lib/python2.6/site-packages/nose-1.1.2-py2.6.egg/nose/case.py", > line 197, in runTest > self.test(*self.arg) > File > "/home/nelle/Projets/skimage/skimage/transform/tests/test_project.py", line > 23, in test_homography > x90 = homography(x, M, order=1) > File "/home/nelle/Projets/skimage/skimage/transform/project.py", line > 101, in homography > mode=mode, order=order, cval=cval) > File > "/home/nelle/Projets/skimage/env/lib/python2.6/site-packages/scipy-0.9.0-py2.6-linux-i686.egg/scipy/ndimage/interpolation.py", > line 298, in map_coordinates > output, order, mode, cval, None, None) > RuntimeError: data type not supported > > Thanks, > Nelle > > Hi Nelle, Thanks for working on this. I actually don't have any test failures when I check out your branch. Nose reports 227 tests run (4 skips, but the skips are b/c I don't have pyfits on my machine). I'm running cython 14.1 and numpy dev (and scipy dev), so my system isn't exactly a match. But I can't imagine how these differences could change the test behavior before and after the renaming. Are you sure the test passed before the rename? Also, if anyone else wants to test this branch, just note that git acts a little weird with it. When I checkout the skimage branch, it adds the skimage tree, but doesn't remove the scikits.image tree (which can cause build/test problems). Similarly, switching back adds the scikits.image tree, but doesn't remove the skimage tree. You'll need to manually remove these before building/testing. Best, -Tony

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