scikit-image March 2013

scikit-image@python.org

16 participants
37 discussions

imageio progress
by Almar Klein 27 Mar '13

27 Mar '13

Dear all, Several months ago, I decided to take the code for skimage's freeimage plugin (which was originally written by Zach Pincus) and turn it into a stand-alone library. I discussed with Zach and a few others how to proceed with that, and it seemed that time was a limiting factor for many, so I ended up doing most coding on my own. The project is called imageio <http://imageio.readthedocs.org/> and it is now a plugin-based library with a relatively small core. The freeimage plugin that started it all currently provides most file formats. Its now at a stage where I think the core is pretty much finished, and focus can shift towards different plugins for various scientific formats. But I am not going to do that alone :) I could use some help with: * People just trying it out. * People checking the design of the classes<http://imageio.readthedocs.org/en/latest/classes.html>and plugin system <http://imageio.readthedocs.org/en/latest/plugins.html>. * If possible, people checking out the code a bit. * And of course, people writing plugins! The way I see it, imageio can become a common backend for reading and writing images for several libraries (including skimage), or can function stand-alone. Further, I plan on moving it to github to easier attract developers. Any help and comments is much appreciated, Almar

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Re: 3D SLIC code
by Juan Nunez-Iglesias 14 Mar '13

14 Mar '13

Thanks for not using lmgtfy, Johannes. =) I found that page earlier but my eyes glazed over a bit. Will try it out. On Fri, Mar 15, 2013 at 2:11 AM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > On Thu, Mar 14, 2013 at 4:54 PM, Johannes Schönberger > <jschoenberger(a)demuc.de> wrote: > > There is a short introduction to debugging Cython: > > > > http://docs.cython.org/src/userguide/debugging.html > > Thanks for this--I wasn't even aware of cygdb! > > 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. > > >

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Re: 3D SLIC code
by Johannes Schönberger 14 Mar '13

14 Mar '13

There is a short introduction to debugging Cython: http://docs.cython.org/src/userguide/debugging.html Johannes Schönberger Am 14.03.2013 um 15:41 schrieb Juan Nunez-Iglesias <jni.soma(a)gmail.com>: > Anyone got tips for debugging Cython code? My usual approach of calling a function using pdb.run() inside iPython isn't working very well. =) > > -- > 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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[JOB] 18 months contract on Python/Qt for microscopy
by Jerome Kieffer 14 Mar '13

14 Mar '13

Dear Pythonistas I would like to advertise about a job proposition at the European synchrotron (Grenoble, France). It is a position for building the software part of the most powerful "X-ray nanoscope" (NiNa ID16/ESRF) for 18 months. Skills: Python/Qt/C++ Developer More info on: http://esrf.profilsearch.com/recrute/intranet/fo_annonce_voir.php?id=198 Cheers -- Jerome Kieffer <google(a)terre-adelie.org>

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Re: 3D SLIC code
by Juan Nunez-Iglesias 14 Mar '13

14 Mar '13

Anyone got tips for debugging Cython code? My usual approach of calling a function using pdb.run() inside iPython isn't working very well. =)

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Re: 3D SLIC code
by Juan Nunez-Iglesias 11 Mar '13

11 Mar '13

> On Mon, Mar 11, 2013 at 8:32 PM, Colin Lea <colincsl(a)gmail.com> wrote: > >> Seems like a silly question, but when you say 3D you mean an RGB image >> right? I work with kinect data everyday so I originally thought you were >> talking about incorporating depth data. > > Currently SLIC supports 2D grayscale and 2D RGB. I want to add support for 3D grayscale and 3D RGB, indeed incorporating depth information. (Though for 3D microscopy, which is pretty different from Kinect!)

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Re: 3D SLIC code
by Colin Lea 11 Mar '13

11 Mar '13

Seems like a silly question, but when you say 3D you mean an RGB image right? I work with kinect data everyday so I originally thought you were talking about incorporating depth data. On Monday, March 11, 2013 4:13:52 AM UTC-4, Ronnie Ghose wrote: > > Thanks. > > > On Mon, Mar 11, 2013 at 4:03 AM, Stéfan van der Walt <ste...(a)sun.ac.za<javascript:> > > wrote: > >> On Mon, Mar 11, 2013 at 10:00 AM, Juan Nunez-Iglesias >> <jni....(a)gmail.com <javascript:>> wrote: >> > Also, I intend to assume isotropic 3D to begin with, and add support for >> > non-isotropic data in a subsequent PR... Does that make sense? Or do you >> > prefer I do it all at once? >> >> Let's do them one step at a time. Thanks, Juan! >> >> 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...(a)googlegroups.com <javascript:>. >> For more options, visit https://groups.google.com/groups/opt_out. >> >> >> >

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Re: 3D SLIC code
by Ronnie Ghose 11 Mar '13

11 Mar '13

Thanks. On Mon, Mar 11, 2013 at 4:03 AM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > On Mon, Mar 11, 2013 at 10:00 AM, Juan Nunez-Iglesias > <jni.soma(a)gmail.com> wrote: > > Also, I intend to assume isotropic 3D to begin with, and add support for > > non-isotropic data in a subsequent PR... Does that make sense? Or do you > > prefer I do it all at once? > > Let's do them one step at a time. Thanks, Juan! > > 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. > > >

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Re: 3D SLIC code
by Stéfan van der Walt 11 Mar '13

11 Mar '13

On Mon, Mar 11, 2013 at 10:00 AM, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: > Also, I intend to assume isotropic 3D to begin with, and add support for > non-isotropic data in a subsequent PR... Does that make sense? Or do you > prefer I do it all at once? Let's do them one step at a time. Thanks, Juan! Stéfan

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Re: 3D SLIC code
by Juan Nunez-Iglesias 11 Mar '13

11 Mar '13

Ok so I interpret that we have a consensus of the following: 1) Use a "multichannel" named argument that defaults to True, rather than try some fancy guesswork based on the input data dimension. 2) Make 2D a special case of 3D to keep codebase simple, at a performance cost relative to a pure 2D implementation. I'll go ahead with this implementation unless someone objects... Also, I intend to assume isotropic 3D to begin with, and add support for non-isotropic data in a subsequent PR... Does that make sense? Or do you prefer I do it all at once? On Mon, Mar 11, 2013 at 6:52 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > On Mon, Mar 11, 2013 at 9:39 AM, Ronnie Ghose <ronnie.ghose(a)gmail.com> > wrote: > > ... ehhh... I would prefer 2d rgb to be the default in general as I think > > that is the generl use case? . This calls for a discussion imho. > > Yes, I think for this algorithm you're right. > > 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. > > >

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scikit-image March 2013