Mailman 3 April 2013 - scikit-image

Annoying gstreamer bug
by Juan Nunez-Iglesias 09 Apr '13

09 Apr '13

Hi All, Consider the following code, saved in a file called test.py: import gst I will bet that few among you would predict this output: $ python test.py -h Usage: test.py [OPTION...] - GStreamer initialization Help Options: -h, --help Show help options --help-all Show all help options --help-gst Show GStreamer Options It seems that someone forgot an if __name__ == '__main__' guard somewhere! Now, this would be none of our concern except for the following corollary: $ python -c 'from skimage.io.collection import alphanumeric_key' -h Usage: -c [OPTION...] - GStreamer initialization Help Options: -h, --help Show help options --help-all Show all help options --help-gst Show GStreamer Options Now, I don't know how to fix this, because it make sense that `io` would import `video` (although `from .video import *` is sloppy). But any suggestions are very very welcome. Juan.

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Re: Histogram backprojection
by Stéfan van der Walt 09 Apr '13

09 Apr '13

On Tue, Apr 9, 2013 at 6:51 PM, abid rahman <abidrahman2(a)gmail.com> wrote: >> > http://opencvpython.blogspot.in/2013/03/histograms-4-back-projection.html. I got hold of it now, thanks. That looks very interesting, as does http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.132.5942 We look forward to your pull request! Let us know if you need any help. Regards Stéfan

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Re: Histogram backprojection
by abid rahman 09 Apr '13

09 Apr '13

Sorry about that. I don't know what is the problem. It works fine for me. Please try base url : www.opencvpython.blogspot.in On Tue, Apr 9, 2013 at 10:18 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > Hi Abid > > On Tue, Apr 9, 2013 at 6:40 PM, abid rahman <abidrahman2(a)gmail.com> wrote: > > I would like to add a feature on histogram backprojection as proposed by > > Swain & Michael J. in their paper "Indexing via color histograms".. > Earlier, > > I had written a simple article on that ( it was focussed for OpenCV) in > my > > blog : > > > http://opencvpython.blogspot.in/2013/03/histograms-4-back-projection.html. > > For some reason, I get a blank blog entry page when I try to load > that. Can anyone else see it? > > 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. > > > -- Abid K. opencvpython.blogspot.com

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Re: Histogram backprojection
by Puneeth Chaganti 09 Apr '13

09 Apr '13

On Tue, Apr 9, 2013 at 10:18 PM, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: > Hi Abid > > On Tue, Apr 9, 2013 at 6:40 PM, abid rahman <abidrahman2(a)gmail.com> wrote: >> I would like to add a feature on histogram backprojection as proposed by >> Swain & Michael J. in their paper "Indexing via color histograms".. Earlier, >> I had written a simple article on that ( it was focussed for OpenCV) in my >> blog : >> http://opencvpython.blogspot.in/2013/03/histograms-4-back-projection.html. > > For some reason, I get a blank blog entry page when I try to load > that. Can anyone else see it? It takes a short while (~20s?) to load. But, I can see it.

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Re: GSOC 2013 Proposal
by Stéfan van der Walt 09 Apr '13

09 Apr '13

Hi Siddharth On Tue, Apr 9, 2013 at 11:32 AM, siddharth kherada <siddharthkherada27(a)gmail.com> wrote: > I am currently pursuing MS by Research in the field of image processing at > IIIT- Hyderabad, India. I am interested in working for Scikit-image this > summer in a GSoC project. Thanks for getting in touch. Both these algorithms are cute, and we'll consider PRs for them if they come in, but I don't think they are major underlying parts of the library we'd want to spend a GSoC on. If you are interested in this sort of thing, image deconvolution may be more relevant. For GSoC, we'd like to implement algorithms that will be useful across a wide array of disciplines, if possible. Also, we require that students who would like to participate in GSoC first make other contributions to the project, so be sure to look at the list of tickets and try to fix some of them, at a minimum. Regards Stéfan

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Re: [OT] open-data movies of science experiments
by Marianne Corvellec 07 Apr '13

07 Apr '13

Hi Emmanuelle, On the biology side again (but biophysics is a big thing ;)), I'm fascinated with the OpenSPIM project and their data might be suitable: http://openspim.org/Gallery#OpenSPIM_data I haven't checked though. Marianne

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[OT] open-data movies of science experiments
by Emmanuelle Gouillart 06 Apr '13

06 Apr '13

Hello, sorry for the slightly off-topic e-mail. I'm currently working on a tutorial on image processing with skimage aimed at undergraduate physics teachers. To show them how skimage can be useful for them and their students, I wish to process images taken from a video of a physics experiment (Brownian motion of particles, granular segregation / Brazil nut effect, rising of bubbles in a viscous fluids etc.). However, I'm having a hard time finding open data with a suitable license (such as creative commons). Would you know a website that gathers a large number of open-data educational / scientific movies, and in particular of science experiments? That'd be very helpful. Cheers, Emmanuelle

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Re: imageio progress
by Ralf Gommers 06 Apr '13

06 Apr '13

On Wed, Mar 27, 2013 at 3:33 PM, Almar Klein <almar.klein(a)gmail.com> wrote: > 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, > Hi Almar, this looks interesting. I'm not really working with images anymore, but was tempted to try imageio out anyway. Installation was smooth, and the 16-bit TIFF image I tried loaded just fine (where PIL still chokes). So in it's current form I suspect it's already quite useful for some people. I haven't looked in enough detail to be able to comment on the classes/plugin design. An option to use imageio.imread/imsave (and/or skimage.io.imread/imsave) as an alternative to PIL from scipy.misc.imread/imshow would make sense to me. Cheers, Ralf

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Re: SciPy 2013 Tutorial
by Emmanuelle Gouillart 06 Apr '13

06 Apr '13

Hi Tony, I've heard that there has been a deadline extension (from people that were also behind schedule for submitting their tutorial :-), so I think it's still time to submit an abstract. Cheers, Emmanuelle On Mon, Apr 01, 2013 at 10:26:07PM -0500, Tony Yu wrote: > Emmanuelle, > Thanks so much for passing along your proposal... Unfortunately, I got > caught up with other things and didn't have time to put together a > proposal for SciPy. :( > -Tony > On Fri, Mar 29, 2013 at 2:51 AM, Emmanuelle Gouillart > <[1]emmanuelle.gouillart(a)nsup.org> wrote: > Hi Tony, > I'm not going to SciPy 2013, but I've agreed to give a 1h30-long > tutorial > on image processing with scikit-image at Euroscipy 2013 (August 21-24). > I'd happy to share course materials if you're interested. > I copy below the abstract I've given to the organizers. > Cheers, > Emmanuelle > Image processing with scikit-image and the SciPy stack > ====================================================== > Numerical image processing involves the manipulation and transformation > of images, often in order to extract information of interest from the > images. NumPy nd-arrays provide an efficient container for image data, > that can therefore be processed using the SciPy toolstack. > In this tutorial, we will first briefly see how simple operations on > images (e.g. cropping, framing) can be performed using NumPy. More > complex image processing operations will be handled principally by the > scikit-image module (occasionally by the ndimage submodule of > SciPy). Compared to other image processing modules for Python, > scikit-image is designed to work transparently with numpy nd-arrays, and > is written in pure Python and some Cython in order to promote > readability > and maintainability. > The different subtopics of this tutorial include: > * input and output of images (file formats...) > * image enhancing / denoising > * image segmentation (separating an image in labeled regions) > * extraction of geometrical features (edges, lines, spheres, > skeleton...) > * extraction of features for image classification > This tutorial will consist mostly of hands-on examples; no mathematical > justification of the algorithms will be given during the tutorial. > Besides the main image processing tasks, the tutorial will demonstrate > how NumPy advanced features (masks, broadcasting, manipulation of > subsets of indices) and scikit-image utilities functions make image > processing easier. The tutorial will also address the visualization of > image processing results (contours, etc.). > On Thu, Mar 28, 2013 at 09:06:04PM -0500, Tony Yu wrote: > > � �I was wondering if anyone has plans to submit a [1]tutorial > proposal for > > � �SciPy 2013. The proposal is due on Monday (Apr. 1st). It'd be great > to > > � �have scikit-image represented there; especially since medical > imaging is > > � �one of the mini-symposia topics. > > � �If no one else is able, I'll probably submit something, but I have > a > > � �feeling that many of you have more (i.e. any) experience teaching > image > > � �processing than I do. > > � �Cheers, > > � �-Tony

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Re: [OT] open-data movies of science experiments
by Emmanuelle Gouillart 06 Apr '13

06 Apr '13

On Sat, Apr 06, 2013 at 02:13:56PM +0200, Nelle Varoquaux wrote: > > Would you know a website that gathers a large number of open-data > > educational / scientific movies, and in particular of science > > experiments? That'd be very helpful. > Would you be interested in live cell imaging ? Well, this is not what I was primarily looking for (my audience will consist mostly of physics teachers) but it could be interesting for other training sessions, or for the biology teachers. Do you know such a website for live cell imaging? Thanks for your help, Emmanuelle

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