scikit-image January 2014

scikit-image@python.org

20 participants
46 discussions

Re: Non-local means denoising
by Kevin Keraudren 23 Jan '14

23 Jan '14

Hi, Here are some implementations of Non-Local Means Denoising you might be interested in for reference/comparison: Image Processing On Line Journal (Antoni Buades, Bartomeu Coll, and Jean-Michel Morel): http://www.ipol.im/pub/art/2011/bcm_nlm/ Pierrick CoupÃ©'s website: https://sites.google.com/site/pierrickcoupe/softwares/denoising-for-medical… ITK implementation in the Baby Brain Toolkit, from FranÃ§ois Rousseau: https://github.com/rousseau/fbrain/blob/master/Code/Denoising/btkNLMTool.txx The first one provides an online demo, is easy to wrap in cython, but is only 2D whereas the two others handle 3D images. Kind regards, Kevin Le 23/01/2014 02:37, Matthew Trentacoste a Ã©crit : > I've looked at the paper a bit. That might actually be up my alley. > Let me reread and get back to you. > > > On Wed, Jan 22, 2014 at 5:05 PM, StÃ©fan van der Walt <stefan(a)sun.ac.za > <mailto:stefan@sun.ac.za>> wrote: > > Hi all, > > Has anyone taken a look at non-local means denoising? It would make > for a good PR. > > StÃ©fan > > -- > 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 > <mailto:scikit-image%2Bunsubscribe@googlegroups.com>. > For more options, visit https://groups.google.com/groups/opt_out. > > > > > -- > > [ matthew m trentacoste ] > [ ] > [ mt(a)matttrent.com <mailto:mt@matttrent.com> ] > [ http://matttrent.com ] > [ twitter: @matttrent ] > [ +1.415.326.3226 ] > -- > 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/groups/opt_out.

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Re: Non-local means denoising
by Matthew Trentacoste 22 Jan '14

22 Jan '14

I've looked at the paper a bit. That might actually be up my alley. Let me reread and get back to you. On Wed, Jan 22, 2014 at 5:05 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > Hi all, > > Has anyone taken a look at non-local means denoising? It would make > for a good PR. > > 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/groups/opt_out. > -- [ matthew m trentacoste ] [ ] [ mt(a)matttrent.com ] [ http://matttrent.com ] [ twitter: @matttrent ] [ +1.415.326.3226 ]

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Non-local means denoising
by Stéfan van der Walt 22 Jan '14

22 Jan '14

Hi all, Has anyone taken a look at non-local means denoising? It would make for a good PR. Stéfan

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Re: Help with Travis
by Jonathan Helmus 21 Jan '14

21 Jan '14

Juan, You also might want to look into using a testing framework such as nose (https://nose.readthedocs.org/en/latest/) for running your unit tests. A number of scientific python packages use this package including scikit-image. If you name the file and functions/classes containing your unit tests correctly, nose will automatically collect and run your tests. In addition, you can use the handy nosetests command which will set the exit value correctly. If you look at the .travis.yml file for scikits-image you will see that on line 66 nosetests is used to run runs the unit tests. This same method is used in many other scientific python packages Cheers, - Jonathan On 01/21/2014 12:06 AM, Ralf Gommers wrote: > > > > On Tue, Jan 21, 2014 at 2:00 AM, Juan Nunez-Iglesias > <jni.soma(a)gmail.com <mailto:jni.soma@gmail.com>> wrote: > > Hi guys, > > A bit off-topic but I hope someone will be able to help trivially... > > I'm trying to run Travis on my own gala repository (you might > remember gala from my scipy2012 talk, when it was called ray). It > appeared to be working fine, but actually it's giving me a little > green dot when in fact a bunch of tests are failing! > > https://travis-ci.org/jni/gala/builds/16860892 > > > Last line:"Done. Your build exited with 0." > > > Here's the corresponding .travis.yml file: > > https://github.com/jni/gala/blob/tree-agglo/.travis.yml > > What am I doing wrong? How can I make it so the test failures > result in build failures? > > > You need your test script to have a nonzero exit status. You also need > to run all your tests from a single script for that to work properly. > You could copy and adapt > https://github.com/scipy/scipy/blob/master/runtests.py for your project. > > Cheers, > Ralf > > > > Thanks, > > 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 > <mailto:scikit-image%2Bunsubscribe@googlegroups.com>. > For more options, visit https://groups.google.com/groups/opt_out. > > > -- > 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/groups/opt_out.

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Access to PowerPC platform
by Stéfan van der Walt 21 Jan '14

21 Jan '14

Hi, Does anyone have access to a PowerPC machine? It would be helpful to have a backtrace on the following error in FreeImage: https://buildd.debian.org/status/fetch.php?pkg=skimage&arch=powerpc&ver=0.9… Thanks Stéfan

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Re: Help with Travis
by Ralf Gommers 20 Jan '14

20 Jan '14

On Tue, Jan 21, 2014 at 2:00 AM, Juan Nunez-Iglesias <jni.soma(a)gmail.com>wrote: > Hi guys, > > A bit off-topic but I hope someone will be able to help trivially... > > I'm trying to run Travis on my own gala repository (you might remember > gala from my scipy2012 talk, when it was called ray). It appeared to be > working fine, but actually it's giving me a little green dot when in fact a > bunch of tests are failing! > > https://travis-ci.org/jni/gala/builds/16860892 > Last line: "Done. Your build exited with 0." > > Here's the corresponding .travis.yml file: > > https://github.com/jni/gala/blob/tree-agglo/.travis.yml > > What am I doing wrong? How can I make it so the test failures result in > build failures? > You need your test script to have a nonzero exit status. You also need to run all your tests from a single script for that to work properly. You could copy and adapt https://github.com/scipy/scipy/blob/master/runtests.pyfor your project. Cheers, Ralf > Thanks, > > 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/groups/opt_out. >

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Help with Travis
by Juan Nunez-Iglesias 20 Jan '14

20 Jan '14

Hi guys, A bit off-topic but I hope someone will be able to help trivially... I'm trying to run Travis on my own gala repository (you might remember gala from my scipy2012 talk, when it was called ray). It appeared to be working fine, but actually it's giving me a little green dot when in fact a bunch of tests are failing! https://travis-ci.org/jni/gala/builds/16860892 Here's the corresponding .travis.yml file: https://github.com/jni/gala/blob/tree-agglo/.travis.yml What am I doing wrong? How can I make it so the test failures result in build failures? Thanks, Juan.

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Review of PR : FAST and ORB
by Ankit Agrawal 19 Jan '14

19 Jan '14

Hi all, The FAST and ORB pull request<https://github.com/scikit-image/scikit-image/pull/834>needs a final round of review. Johannes is done with some crucial design changes on the original PR<https://github.com/scikit-image/scikit-image/pull/699>. Please review it if you have some time. This might sound pretty lame, but merging this PR will motivate me to complete the work on FREAK descriptor<https://github.com/scikit-image/scikit-image/pull/729>. Thank you. Regards, Ankit.

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Re: scikit-image paper
by Johannes Schönberger 18 Jan '14

18 Jan '14

@Juan That'd be great :-) On Sat, Jan 18, 2014 at 9:28 PM, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: > Thanks for the ping, Johannes! I myself dropped the ball on this but ready > to pick it up again! > > > On Sun, Jan 19, 2014 at 3:24 AM, Johannes Schönberger <jsch(a)demuc.de> wrote: >> >> Good to hear. >> >> Let me know how to improve the Development section and I could certainly >> contribute another example - not sure how many examples we want to include? >> >> On Jan 18, 2014, at 4:30, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: >> >> > Johannes, sorry for the delay on this; the paper is a top priority for >> > me, and I should have quite a bit of time to work on this starting Sunday >> > evening. >> > >> > >> > -- >> > 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/groups/opt_out. >> >> -- >> 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/groups/opt_out. > > > -- > 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/groups/opt_out.

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Re: scikit-image paper
by Johannes Schönberger 18 Jan '14

18 Jan '14

Good to hear. Let me know how to improve the Development section and I could certainly contribute another example - not sure how many examples we want to include? On Jan 18, 2014, at 4:30, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: > Johannes, sorry for the delay on this; the paper is a top priority for me, and I should have quite a bit of time to work on this starting Sunday evening. > > > -- > 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/groups/opt_out.

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scikit-image January 2014