scikit-image August 2012

scikit-image@python.org

11 participants
40 discussions

Re: Sprint
by Stéfan van der Walt 26 Aug '12

26 Aug '12

Thanks, Nicolas--this is going to help a lot! Forwarding to the list as well. Regards Stéfan On Sun, Aug 26, 2012 at 6:20 AM, Nicolas Rougier <Nicolas.Rougier(a)inria.fr> wrote: > > Hi, > > > I've tried to post to the mailing list but for some reason my message did not appear (feel free to forward this one to the list). > > For text, there are the freetype-py bindings available from http://code.google.com/p/freetype-py/ > > Be sure to check the example directory that explain how to render text once you've chosen a font file. > By default, I generally use the Bitstream Vera family that might be BSD compatible (but I'm not so sure). > > Also, there is a nice article on text rendering: http://www.antigrain.com/research/font_rasterization/ > The "agg_trick.py" demo does just that. > > In the end, you get a RGBA array with the text within so it should be easy to add it to an image. > > > > Also, I read you need bezier curves and I recently translated the bezier curve code from the antigrain library: > > http://www.antigrain.com/research/adaptive_bezier/index.html > > > You can find at http://code.google.com/p/gl-agg/source/browse/python/gl-curve.py two functions: > > curve3_bezier( P1, P2, P3 ) and curve4_bezier( P1, P2, P3, P4) that takes respectively 3 and 4 points as input and will give you back a list of points. If you draw straight lines between those points, then you're done with bezier. > > > > > Nicolas > >

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Re: Cython version to build master
by Andreas Mueller 25 Aug '12

25 Aug '12

On 08/25/2012 07:27 PM, Tony Yu wrote: > > > On Sat, Aug 25, 2012 at 1:19 PM, Andreas Mueller > <amueller(a)ais.uni-bonn.de <mailto:amueller@ais.uni-bonn.de>> wrote: > > I just saw the commit with the change in the docs. > Is this because of the memory views? Can someone point me to the > discussion? > Not being able to build scikits-image on current Ubuntu seems a > bit annoying to me. > > > Argh. I didn't realize this. I think it would probably be a good > policy if the current Ubuntu version sets a *maximum* version on our > dependencies. > > -T > Yeah, I think that is a good idea. I think Ubuntu and Debian are used by many researchers and as long as it doesn't hold us back, I think it is a good idea to support some versions back - and definitely the current.

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Cython version to build master
by Andreas Mueller 25 Aug '12

25 Aug '12

Hi everybody. I haven't kept track of all of the many PRs this last weeks, but I noticed today that I can't build master. There is an error in "skimage/morphology/_greyreconstruct.pyx". I guess that is because I use Cython 0.15.1. Is that correct? Do we only support Cython 0.16 now? Cheers, Andy

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Re: Qt-MPL image viewer
by Stéfan van der Walt 24 Aug '12

24 Aug '12

Hi Tony On Sat, Jul 28, 2012 at 7:08 AM, Tony Yu <tsyu80(a)gmail.com> wrote: > So I've been hacking on a new implementation of an > image-viewer/interactive-image-processor. See PR 229: > > https://github.com/scikits-image/scikits-image/pull/229 This is great! I've played around with the PR, and I love the simplicity of the API. It's now been merged into master. > P.S. Stefan: In a separate branch, I've added the Hough Transform plugin you > so desired. Ah, neat! I'm going to try that right now. Stéfan

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Re: Bundling scikits-image using pyinstaller
by Stéfan van der Walt 24 Aug '12

24 Aug '12

Hi Nicklas, On Tue, Jul 31, 2012 at 2:16 AM, Nicklas Nordenmark <nordenmark(a)gmail.com> wrote: > From the Pyinstaller manual > (http://www.pyinstaller.org/export/develop/project/doc/Manual.html?format=raw): > >> In most sophisticated apps, it becomes necessary to figure out (at >> runtime) whether you're running "live" or "frozen". For example, you might >> have a configuration file that (running "live") you locate based on a >> module's __file__ attribute. That won't work once the code is packaged up. >> You'll probably want to look for it based on sys.executable instead. Would you be interested in preparing a pull-request to handle this issue? Regards Stéfan

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Re: Questions about hog.py file
by Stéfan van der Walt 24 Aug '12

24 Aug '12

On Mon, Aug 6, 2012 at 6:31 AM, Omar Trinidad Gutiérrez Méndez <omar.vpa(a)gmail.com> wrote: > I am reading the source code of the file hog.py, I found the next line of > code: > > n_cellsx = int(np.floor(sx // cx)) > > I don't know why they join the NumPy function floor and the // operator. Is > there any reason to do this? I can't see. I feel that is doing the same > thing twice. I never followed up on this; has the issue been addressed by the latest HoG fixes? Stéfan

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Re: bug in regionprops underlying library qhull?
by Luca Fiaschi 24 Aug '12

24 Aug '12

Hi, I confirm the bug to be really in qhull. I substituted the computation of the convex hull in scipy (qhull) with another library (vigranumpy) and thins fix the problem. If useful I might consider working on a cython implementation of the 2D convex hull algorithm and flash a pull request. Best Luca Il giorno martedì 21 agosto 2012 12:40:39 UTC+2, Luca Fiaschi ha scritto: > > Hi all, > I get a strange bug trying to uses regionprops on some images. > Computing the hull of some objects result a internal error in the qhull > library: > Below you can find the error and and the set of points which triggers it: > > Does anybody know how to fix it? > > > [[ 5. 12.5] > [ 6. 6.5] > [ 7. 4.5] > [ 8. 4.5] > [ 9. 4.5] > [ 10. 5.5] > [ 7. 4.5] > [ 7. 5.5] > [ 6. 6.5] > [ 6. 7.5] > [ 6. 8.5] > [ 6. 9.5] > [ 6. 10.5] > [ 6. 11.5] > [ 5. 12.5] > [ 5. 13.5] > [ 5. 14.5] > [ 5. 15.5] > [ 5. 16.5] > [ 5. 17.5] > [ 5. 18.5] > [ 5. 19.5] > [ 5. 20.5] > [ 5. 21.5] > [ 5. 22.5] > [ 5. 23.5] > [ 5. 24.5] > [ 6. 25.5] > [ 5. 24.5] > [ 6. 25.5] > [ 7. 25.5] > [ 8. 23.5] > [ 9. 20.5] > [ 10. 16.5] > [ 9. 4.5] > [ 10. 5.5] > [ 10. 6.5] > [ 10. 7.5] > [ 10. 8.5] > [ 10. 9.5] > [ 10. 10.5] > [ 10. 11.5] > [ 10. 12.5] > [ 10. 13.5] > [ 10. 14.5] > [ 10. 15.5] > [ 10. 16.5] > [ 9. 17.5] > [ 9. 18.5] > [ 9. 19.5] > [ 9. 20.5] > [ 8. 21.5] > [ 8. 22.5] > [ 8. 23.5] > [ 7. 24.5] > [ 7. 25.5] > [ 5. 13.5] > [ 6. 7.5] > [ 7. 5.5] > [ 8. 5.5] > [ 9. 5.5] > [ 10. 6.5] > [ 7. 5.5] > [ 7. 6.5] > [ 6. 7.5] > [ 6. 8.5] > [ 6. 9.5] > [ 6. 10.5] > [ 6. 11.5] > [ 6. 12.5] > [ 5. 13.5] > [ 5. 14.5] > [ 5. 15.5] > [ 5. 16.5] > [ 5. 17.5] > [ 5. 18.5] > [ 5. 19.5] > [ 5. 20.5] > [ 5. 21.5] > [ 5. 22.5] > [ 5. 23.5] > [ 5. 24.5] > [ 5. 25.5] > [ 6. 26.5] > [ 5. 25.5] > [ 6. 26.5] > [ 7. 26.5] > [ 8. 24.5] > [ 9. 21.5] > [ 10. 17.5] > [ 9. 5.5] > [ 10. 6.5] > [ 10. 7.5] > [ 10. 8.5] > [ 10. 9.5] > [ 10. 10.5] > [ 10. 11.5] > [ 10. 12.5] > [ 10. 13.5] > [ 10. 14.5] > [ 10. 15.5] > [ 10. 16.5] > [ 10. 17.5] > [ 9. 18.5] > [ 9. 19.5] > [ 9. 20.5] > [ 9. 21.5] > [ 8. 22.5] > [ 8. 23.5] > [ 8. 24.5] > [ 7. 25.5] > [ 7. 26.5] > [ 4.5 13. ] > [ 5.5 7. ] > [ 6.5 5. ] > [ 7.5 5. ] > [ 8.5 5. ] > [ 9.5 6. ] > [ 6.5 5. ] > [ 6.5 6. ] > [ 5.5 7. ] > [ 5.5 8. ] > [ 5.5 9. ] > [ 5.5 10. ] > [ 5.5 11. ] > [ 5.5 12. ] > [ 4.5 13. ] > [ 4.5 14. ] > [ 4.5 15. ] > [ 4.5 16. ] > [ 4.5 17. ] > [ 4.5 18. ] > [ 4.5 19. ] > [ 4.5 20. ] > [ 4.5 21. ] > [ 4.5 22. ] > [ 4.5 23. ] > [ 4.5 24. ] > [ 4.5 25. ] > [ 5.5 26. ] > [ 4.5 25. ] > [ 5.5 26. ] > [ 6.5 26. ] > [ 7.5 24. ] > [ 8.5 21. ] > [ 9.5 17. ] > [ 8.5 5. ] > [ 9.5 6. ] > [ 9.5 7. ] > [ 9.5 8. ] > [ 9.5 9. ] > [ 9.5 10. ] > [ 9.5 11. ] > [ 9.5 12. ] > [ 9.5 13. ] > [ 9.5 14. ] > [ 9.5 15. ] > [ 9.5 16. ] > [ 9.5 17. ] > [ 8.5 18. ] > [ 8.5 19. ] > [ 8.5 20. ] > [ 8.5 21. ] > [ 7.5 22. ] > [ 7.5 23. ] > [ 7.5 24. ] > [ 6.5 25. ] > [ 6.5 26. ] > [ 5.5 13. ] > [ 6.5 7. ] > [ 7.5 5. ] > [ 8.5 5. ] > [ 9.5 5. ] > [ 10.5 6. ] > [ 7.5 5. ] > [ 7.5 6. ] > [ 6.5 7. ] > [ 6.5 8. ] > [ 6.5 9. ] > [ 6.5 10. ] > [ 6.5 11. ] > [ 6.5 12. ] > [ 5.5 13. ] > [ 5.5 14. ] > [ 5.5 15. ] > [ 5.5 16. ] > [ 5.5 17. ] > [ 5.5 18. ] > [ 5.5 19. ] > [ 5.5 20. ] > [ 5.5 21. ] > [ 5.5 22. ] > [ 5.5 23. ] > [ 5.5 24. ] > [ 5.5 25. ] > [ 6.5 26. ] > [ 5.5 25. ] > [ 6.5 26. ] > [ 7.5 26. ] > [ 8.5 24. ] > [ 9.5 21. ] > [ 10.5 17. ] > [ 9.5 5. ] > [ 10.5 6. ] > [ 10.5 7. ] > [ 10.5 8. ] > [ 10.5 9. ] > [ 10.5 10. ] > [ 10.5 11. ] > [ 10.5 12. ] > [ 10.5 13. ] > [ 10.5 14. ] > [ 10.5 15. ] > [ 10.5 16. ] > [ 10.5 17. ] > [ 9.5 18. ] > [ 9.5 19. ] > [ 9.5 20. ] > [ 9.5 21. ] > [ 8.5 22. ] > [ 8.5 23. ] > [ 8.5 24. ] > [ 7.5 25. ] > [ 7.5 26. ]] > QH6228 > Qhull internal error (qh_findbestlower): all neighbors of facet 12 are > flipped or upper Delaunay. > Please report this error to qhull_bug(a)qhull.org with the input and all of > the output. > ERRONEOUS FACET: > - f12 > - flags: top simplicial upperDelaunay > - normal: -0.965 -0.1942 0.1764 > - offset: 6.243641 > - vertices: p138(v7) p224(v3) p112(v0) > - neighboring facets: f6 f28 f13 > > While executing: | qhull d Qz Qbb Qt > Options selected for Qhull 2010.1 2010/01/14: > run-id 1565793501 delaunay Qz-infinity-point Qbbound-last > Qtriangulate > _pre-merge _zero-centrum Pgood _max-width 22 Error-roundoff 3.7e-14 > _one-merge 2.6e-13 _near-inside 1.3e-12 Visible-distance 7.4e-14 > U-coplanar-distance 7.4e-14 Width-outside 1.5e-13 _wide-facet 4.4e-13 > Last point added to hull was p132. > > At error exit: > > Delaunay triangulation by the convex hull of 225 points in 3-d: > > Number of input sites and at-infinity: 11 > Number of nearly incident points: 9 > Number of Delaunay regions: 0 > > Statistics for: | qhull d Qz Qbb Qt > > Number of points processed: 11 > Number of hyperplanes created: 31 > Number of facets in hull: 18 > Number of distance tests for qhull: 1324 > > > precision problems (corrected unless 'Q0' or an error) > 8 coplanar points during partitioning > >

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Re: EuroSciPy sprint
by Emmanuelle Gouillart 23 Aug '12

23 Aug '12

Thank you Stéfan, I just copied the summary on https://github.com/scikits-image/scikits-image/wiki/Euroscipy-2012-sprint Who is going to participate to the sprint, eventually? If you plan to participate, please add you name on the wiki page. Cheers, Emmanuelle On Thu, Aug 16, 2012 at 02:53:00PM -0700, Stéfan van der Walt wrote: > Thanks for all the suggestions. Here then is the latest sprint summary: > SPRINT: scikits-image > What? > scikits-image is a collection of algorithms for image processing. See > http://scikits-image.org/ for more detail. > When? > Both on Mon Aug 27 and Tue Aug 28 > Whom to contact? > Stéfan van der Walt (stefan(a)sun.ac.za) > Tasks > There are a few outstanding issues that can be fixed easily: > https://github.com/scikits-image/scikits-image/issues?labels=quickfix > Ideas for the sprint: > - Add text, anti-aliasing to the draw module > - Add Bezier curves to the draw module (see the PDF linked from > http://free.pages.at/easyfilter/bresenham.html) > - Integrate Tony's visualization tools, and use them to write a > plugin, or fine-tune the existing Hough parameter space explorer > - Add binary features (BRIEF, BRISK, FREAK, LAZY) > http://computer-vision-talks.com/2011/08/feature-descriptor-comparison-repo… > - Camera calibration > Start from https://gist.github.com/3348000 and > http://bazaar.launchpad.net/~astraw/pinpoint/dev/files/ > - Better video loading > - Update the user guide > We need a “Getting started” section, guiding a user through a > typical workflow: > 1. Load an image > 2. Try using a feature detector or transform. > 3. Realize that it didn't perform ideally. Now try smoothing or > denoising (or something else). > 4. Successfully find feature. > 5. Save feature as some sort of data file. > - Add imread_collection to all imread plugins. > Outstanding challenges: > - Blurring kernel estimation (http://bit.ly/Nril3u) > - “Sudoku challenge” > (http://stackoverflow.com/questions/10196198/how-to-remove-convexity-defects…) > Specific examples to be implemented: > - Corner detection > (http://stackoverflow.com/questions/8686926/python-image-processing-help-nee…)

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Re: Subpackage for utilities
by Johannes Schönberger 21 Aug '12

21 Aug '12

Pull request has been added. Am Montag, 20. August 2012 19:47:00 UTC+2 schrieb Stefan van der Walt: > > On Mon, Aug 20, 2012 at 10:09 AM, Johannes Schönberger > <hannessch...(a)gmail.com <javascript:>> wrote: > >> How about ``skimage._algorithms`` or, based upon another suggestion on > >> this thread, ``skimage._shared``? > > > > ``skimage._shared`` sounds good. If you don't mind I'll add a pull > request for this and add some of the important functions in there. > > Thanks, please go ahead. > > Stéfan >

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Re: Subpackage for utilities
by Johannes Schönberger 20 Aug '12

20 Aug '12

> How about ``skimage._algorithms`` or, based upon another suggestion on > this thread, ``skimage._shared``? ``skimage._shared`` sounds good. If you don't mind I'll add a pull request for this and add some of the important functions in there. Johannes

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scikit-image August 2012