Mailman 3 March 2014 - scikit-image

Re: Desired Image Compression algorithms in scikit-image
by Ankit Agrawal 19 Mar '14

19 Mar '14

On Wed, Mar 19, 2014 at 4:41 AM, Ralf Gommers <ralf.gommers(a)gmail.com>wrote: > > > > On Tue, Mar 18, 2014 at 5:20 PM, Stuart Mumford <stuart(a)mumford.me.uk>wrote: > >> As point of note, if you are looking into doing Python based JPEG200 you >> should look over the glymur project ( >> https://github.com/quintusdias/glymur) which is Python wrappers around >> the OpenJPEG C lib. If you can code the compression algorithm in Python, >> that library might provide you some framework for dealing with the meta >> data and other things(which are in Python in glymur), save you re-inventing >> the wheel. >> > > I just had a look at Glymur, and that's the kind of code that's useful but > you really don't want to write. I suggested JPEG 2000 simply because it's a > well-known wavelet based algorithm. The scope of Ankit's GSoC should be > *algorithms* imho; dealing with file formats, metatdata, etc. would be a > huge time sink and out of scope for both scipy and scikit-image I'd think. > I concur with Ralf. IMHO, the complete implementation of JPEG 2000 is not something I can manage completely in two and a half weeks. Meanwhile, I am going through the most cited paper<https://www.math.purdue.edu/~lucier/692/DJL-image-compression.pdf>that I got in this area 'Image Compression Through Wavelet Transform Coding', which seems big too. I think maybe Josh has knowledge about wavelet based compression techniques? > > >> SunPy has had a lot of contact from the Glymur dev he is a helpful guy. >> >> Stuart >> >> >> On 18 March 2014 16:16, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: >> >>> www.jpeg.org/jpeg2000guide/papers/madamsjp2k.pdf >>> >>> -- >>> 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/d/optout. >>> >> >> -- >> 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/d/optout. >> > > -- > 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/d/optout. >

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Fwd: [euroscipy-org] EuroSciPy 2014 Call for Abstracts
by Nelle Varoquaux 19 Mar '14

19 Mar '14

Hello everyone, A couple of weeks, Euroscipy launched its call for proposal! This year, the conference will take place in Cambridge (UK), from the 27th to 30th of August. Don't hesitate to submit an abstract! For the second year in a row, participants will have the opportunity to submit a paper to the proceedings. Cheers, N ---------- Forwarded message ---------- From: Ralf Gommers <ralf.gommers(a)gmail.com> Date: 5 March 2014 20:37 Subject: [euroscipy-org] EuroSciPy 2014 Call for Abstracts To: Organisation of EuroScipy <euroscipy-org(a)python.org>, conferences(a)python.org, numfocus(a)googlegroups.com, Discussion of Numerical Python <numpy-discussion(a)scipy.org>, SciPy Users List <scipy-user(a)scipy.org> Dear all, EuroSciPy 2014, the Seventh Annual Conference on Python in Science, takes place in Cambridge, UK on 27 - 30 August 2013. The conference features two days of tutorials followed by two days of scientific talks. The day after the main conference, developer sprints will be organized on projects of interest to attendees. The topics presented at EuroSciPy are very diverse, with a focus on advanced software engineering and original uses of Python and its scientific libraries, either in theoretical or experimental research, from both academia and the industry. The program includes keynotes, contributed talks and posters. Submissions for talks and posters are welcome on our website (http://www. euroscipy.org/2014/). In your abstract, please provide details on what Python tools are being employed, and how. The deadline for submission is 14 April 2013. Also until 14 April 2014, you can apply for a sprint session on 31 August 2014. See https://www.euroscipy.org/2014/calls/sprints/ for details. Important dates: April 14th: Presentation abstracts, poster, tutorial submission deadline. Application for sponsorship deadline. May 17th: Speakers selected May 22nd: Sponsorship acceptance deadline June 1st: Speaker schedule announced June 6th, or 150 registrants: Early-bird registration ends August 27-31st: 2 days of tutorials, 2 days of conference, 1 day of sprints We look forward to an exciting conference and hope to see you in Cambridge in August! The EuroSciPy 2014 Team http://www.euroscipy.org/2014/ Conference Chairs -------------------------- Mark Hayes, Cambridge University, UK Didrik Pinte, Enthought Europe, UK Tutorial Chair ------------------- David Cournapeau, Enthought Europe, UK Program Chair -------------------- Ralf Gommers, ASML, The Netherlands Program Committee ----------------------------- Tiziano Zito, Humboldt-Universität zu Berlin, Germany Pierre de Buyl, Université libre de Bruxelles, Belgium Emmanuelle Gouillart, Joint Unit CNRS/Saint-Gobain, France Konrad Hinsen, Centre National de la Recherche Scientifique (CNRS), France Raphael Ritz, Garching Computing Centre of the Max Planck Society, Germany Stéfan van der Walt, Applied Mathematics, Stellenbosch University, South Africa Gaël Varoquaux, INRIA Parietal, Saclay, France Nelle Varoquaux, Mines ParisTech, France Pauli Virtanen, Aalto University, Finland Evgeni Burovski, Lancaster University, UK Robert Cimrman, New Technologies Research Centre, University of West Bohemia, Czech Republic Almar Klein, Cybermind, The Netherlands Organizing Committee ------------------------------ Simon Jagoe, Enthought Europe, UK Pierre de Buyl, Université libre de Bruxelles, Belgium _______________________________________________ euroscipy-org mailing list euroscipy-org(a)python.org https://mail.python.org/mailman/listinfo/euroscipy-org

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Re: Desired Image Compression algorithms in scikit-image
by Ralf Gommers 19 Mar '14

19 Mar '14

On Tue, Mar 18, 2014 at 5:20 PM, Stuart Mumford <stuart(a)mumford.me.uk>wrote: > As point of note, if you are looking into doing Python based JPEG200 you > should look over the glymur project (https://github.com/quintusdias/glymur) > which is Python wrappers around the OpenJPEG C lib. If you can code the > compression algorithm in Python, that library might provide you some > framework for dealing with the meta data and other things(which are in > Python in glymur), save you re-inventing the wheel. > I just had a look at Glymur, and that's the kind of code that's useful but you really don't want to write. I suggested JPEG 2000 simply because it's a well-known wavelet based algorithm. The scope of Ankit's GSoC should be *algorithms* imho; dealing with file formats, metatdata, etc. would be a huge time sink and out of scope for both scipy and scikit-image I'd think. Ralf > SunPy has had a lot of contact from the Glymur dev he is a helpful guy. > > Stuart > > > On 18 March 2014 16:16, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: > >> www.jpeg.org/jpeg2000guide/papers/madamsjp2k.pdf >> >> -- >> 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/d/optout. >> > > -- > 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/d/optout. >

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Re: Desired Image Compression algorithms in scikit-image
by Stuart Mumford 18 Mar '14

18 Mar '14

As point of note, if you are looking into doing Python based JPEG200 you should look over the glymur project (https://github.com/quintusdias/glymur) which is Python wrappers around the OpenJPEG C lib. If you can code the compression algorithm in Python, that library might provide you some framework for dealing with the meta data and other things(which are in Python in glymur), save you re-inventing the wheel. SunPy has had a lot of contact from the Glymur dev he is a helpful guy. Stuart On 18 March 2014 16:16, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: > www.jpeg.org/jpeg2000guide/papers/madamsjp2k.pdf > > -- > 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/d/optout. >

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Re: Desired Image Compression algorithms in scikit-image
by Stéfan van der Walt 18 Mar '14

18 Mar '14

www.jpeg.org/jpeg2000guide/papers/madamsjp2k.pdf

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Re: Desired Image Compression algorithms in scikit-image
by Ankit Agrawal 18 Mar '14

18 Mar '14

@Juan and Stuart : Thanks for chipping in. On Tue, Mar 18, 2014 at 8:42 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > Hi Ankit > > On Tue, Mar 18, 2014 at 1:17 PM, Ankit Agrawal <aaaagrawal(a)gmail.com> > wrote: > > As a part of my proposal on integrating Discrete Wavelet > Transforms > > and related algorithms into scipy.signal, I need some suggestions on some > > image compression algorithms that I can implement into scikit-image in 3 > > weeks. JPEG 2000 that uses DCT is one that is on the cards currently. > Anyone > > with some knowledge on wavelet based image compression techniques can > > comment about some popular algorithms in this area. I am looking into a > few > > papers but I found the literature on this topic relatively dispersed. > > Glad to hear you may be working (partially) on scikit-image again this > summer! > > Yes, part of it is including a private module `_pywt` in scikit-image to support Image Denoising methods, for example Tristan's PR<https://github.com/scikit-image/scikit-image/pull/760> . JPEG2000 is perfect--well established and already supported by external > tools. > I could not find a paper on JPEG 2000. I found this link<http://www.jpeg.org/jpeg2000guide/guide/contents.html>, but unfortunately it is open for members only. Thanks. Good luck, > Stéfan > >

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Project not mentioned on the project ideas page
by syedtabish.a＠gmail.com 18 Mar '14

18 Mar '14

Hi, I am interested in image/signal processing and have a decent exposure to various image processing algorithms. I would love to participate in gsoc'14, however I am not sure if I can submit a proposal as the project I want to work on is not mentioned on the project ideas page. I would like to work on visual saliency<http://www.scholarpedia.org/article/Visual_salience>computation. As of now this module is not implemented in scikit-image. I would love to implement a bunch saliency algorithms for the proposed module. Please suggest if such a project is feasible, and whether I should go ahead with writing an elaborate proposal. Tabish.

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Re: Desired Image Compression algorithms in scikit-image
by Stuart Mumford 18 Mar '14

18 Mar '14

Hey, Just going to chip in and say that having a pure Python (or Cython) JPEG2000 lib would be lovely for SunPy, so the compression is a good step along this path. Stuart On 18 March 2014 13:30, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: > Hi Ankit! Good to hear from you but unfortunately I can't help you out > with this as it's far out of my realm of expertise! Hopefully some of the > other devs will chime in with some suggestions soon. > > Good luck! > > > On Tue, Mar 18, 2014 at 10:17 PM, Ankit Agrawal <aaaagrawal(a)gmail.com>wrote: > >> Hi everyone, >> >> As a part of my proposal<https://github.com/scipy/scipy/wiki/GSoC-2014-:-Discrete-Wavelet-Transform-…>on integrating Discrete Wavelet Transforms and related algorithms into >> scipy.signal, I need some suggestions on some image compression algorithms >> that I can implement into scikit-image in 3 weeks. JPEG 2000 that uses DCT >> is one that is on the cards currently. Anyone with some knowledge on >> wavelet based image compression techniques can comment about some popular >> algorithms in this area. I am looking into a few papers but I found the >> literature on this topic relatively dispersed. Thanks. >> >> Cheers, >> Ankit. >> >> -- >> 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/d/optout. >> > > -- > 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/d/optout. >

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Desired Image Compression algorithms in scikit-image
by Ankit Agrawal 18 Mar '14

18 Mar '14

Hi everyone, As a part of my proposal<https://github.com/scipy/scipy/wiki/GSoC-2014-:-Discrete-Wavelet-Transform-…>on integrating Discrete Wavelet Transforms and related algorithms into scipy.signal, I need some suggestions on some image compression algorithms that I can implement into scikit-image in 3 weeks. JPEG 2000 that uses DCT is one that is on the cards currently. Anyone with some knowledge on wavelet based image compression techniques can comment about some popular algorithms in this area. I am looking into a few papers but I found the literature on this topic relatively dispersed. Thanks. Cheers, Ankit.

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Re: robust ring (and circle) detection algorithm
by Eldad Afik 16 Mar '14

16 Mar '14

Hi Stéfan, Sure! I've never done this before. Are all the relevant instructions in How to contribute to skimage<http://scikit-image.org/docs/dev/contribute.html#how-to-contribute-to-skima…> ? > "a proof of concept illustration" > Working out the examples in the manuscript are good for this? Best regards, Eldad On Thursday, 13 March 2014 23:34:32 UTC+2, Stefan van der Walt wrote: > > Hi Eldad > > On Sun, Mar 9, 2014 at 3:28 PM, Eldad Afik <eldad...(a)gmail.com<javascript:>> > wrote: > > I summarised the work in a manuscript titled: > > "Robust and highly performant ring detection algorithm for 3d particle > > tracking using 2d microscope imaging" (a pre-print is available at > > arXiv:1310.1371). > > NB, it was written minded at potential users and applications rather > than > > computer scientists, which I am not. > > Shall we start working on a pull request with a proof of concept > illustration? > > Stéfan >

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