Mailman 3 December 2014 - scikit-image

Re: How do you keep documentation so nice?
by Juan Nunez-Iglesias 08 Dec '14

08 Dec '14

Hahaha it's not that dumb! I personally have tried to dive into the doc build process a few times but have found it quite opaque, so I wouldn't mind if Stéfan and/or Tony elaborated a bit here about the build system! =) But as to drawing inspiration, I'm pretty sure it's all BSD, which means you can draw even a bit more than that! =) On Mon, Dec 8, 2014 at 11:14 AM, Adam Hughes <hughesadam87(a)gmail.com> wrote: > I'm dumb. It's clearly right there on your github page in "docs". Geez. > It's ok if I draw inspiration from you guys, right? > On Sun, Dec 7, 2014 at 7:11 PM, Adam Hughes <hughesadam87(a)gmail.com> wrote: >> Hi, >> >> I've been working with sphinx api-doc for autogenerating some >> documentation for a package, and the output is a farcry from the nice, >> super-slick layout that scikit-image has. I saw that on the bottom of your >> page, the docs are built with sphinx and bootstrap. Is the source code for >> the documentation available for perusing by chance? I'd love to get some >> insights on how you keep your page so nice and tidy! >> >> -- >> You received this message because you are subscribed to a topic in the >> Google Groups "scikit-image" group. >> To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/scikit-image/k5K6_vanZVI/unsubscribe. >> To unsubscribe from this group and all its topics, 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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How do you keep documentation so nice?
by Adam Hughes 08 Dec '14

08 Dec '14

Hi, I've been working with sphinx api-doc for autogenerating some documentation for a package, and the output is a farcry from the nice, super-slick layout that scikit-image has. I saw that on the bottom of your page, the docs are built with sphinx and bootstrap. Is the source code for the documentation available for perusing by chance? I'd love to get some insights on how you keep your page so nice and tidy!

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scikit-image v0.11 sprint, 12--14 December
by Stefan van der Walt 06 Dec '14

06 Dec '14

Hi everyone On the weekend of 12 to 14 December, we'll be sprinting to release the next version of scikit-image. Since we're spread out all over the world, from Australia to the US, we'll do tag teams as necessary. No matter your level of expertise, we can use your help! In preparation, I'll be triaging tickets for the 0.11 milestone, which you can find here: https://github.com/scikit-image/scikit-image/milestones/0.11 The event will be coordinated via HipChat: https://skimage.hipchat.com (sign-in required, full history) http://www.hipchat.com/gVXougY5x (no sign-in required, no history) I look forward to seeing you there! Regards Stéfan

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Re: scikit-image v0.11 sprint, 12--14 December
by Juan Nunez-Iglesias 06 Dec '14

06 Dec '14

If you log in as guest, and then click on the signup link at the top, it should work. At least that worked for me, but I didn't have a pre-existing HipChat account, so YMMV. At any rate, Stéfan and I are having a nice chat on gitter, so we might stick with that anyway. =) On Sat, Dec 6, 2014 at 11:55 PM, Steven Silvester <steven.silvester(a)gmail.com> wrote: > The problem persists...but I *can* log in as a guest. > On Sat, Dec 6, 2014 at 4:10 AM, Stefan van der Walt <stefan(a)sun.ac.za> > wrote: >> Hi Steven >> >> On 2014-12-06 05:34:00, Steven Silvester <steven.silvester(a)gmail.com> >> wrote: >> > I had the same problem. I'm logged in to Hipchat through another project >> > and I just get redirected to it. >> >> Please try the following link and let me know: >> >> https://skimage.hipchat.com/chat >> >> Stéfan >> >> -- >> You received this message because you are subscribed to a topic in the >> Google Groups "scikit-image" group. >> To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/scikit-image/KtnLZJEV54Y/unsubscribe. >> To unsubscribe from this group and all its topics, 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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Is there a problem with the function points_in_poly ? measure.points_in_poly
by Julien Derr 05 Dec '14

05 Dec '14

Hi everyone, I would like to use the function points_in_poly to test if the point x,y is in the contour cont2 x=0 y=0, but I have the problem with any value of x and y: skimage.measure.points_in_poly(np.array([x,y]),cont2) where cont2 is a contour of type array : but I get the following error: "IndexError: invalid index" it is a little obscure for me, is there a problem with this function, or is it me who don't know how to apply it ? thanks a lot! Julien cont2 ndarray 7879x2: 15758 elems, type `float64`, 126064 bytes (123 kb) In [12]: skimage.measure.points_in_poly(np.array([0,0]),cont2) --------------------------------------------------------------------------- IndexError Traceback (most recent call last) /home/julien/Dropbox/density_seiche/<ipython-input-12-2271d0f2b0ba> in <module>() ----> 1 skimage.measure.points_in_poly(np.array([0,0]),cont2) /usr/local/lib/python2.7/dist-packages/scikit_image-0.11dev-py2.7-linux-x86_64.egg/skimage/measure/_pnpoly.so in skimage.measure._pnpoly.points_in_poly (skimage/measure/_pnpoly.c:2397)() IndexError: invalid index

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Image warping using transform.PolynomialTransform: crazy results
by Herve Bouy 04 Dec '14

04 Dec '14

Hi, I found very few examples for transform.PolynomialTransform on the internet so I hope someone in this group can help me understand what I am doing wrong. If it's not the right place to ask for help, please forgive me! Here is my problem. I have a greyscale image with some curved lines. I want to transform it so the lines become straight. <https://lh3.googleusercontent.com/-l7PV-L6ZCek/VGsf6aKWYpI/AAAAAAAABSk/Pae2…> So I measure the position of the lines at regular intervals (in the attached file source_test2.csv) And compute the desired positions after transformation (in the attached file destination_test2.csv) So i have a nice set of input points and their correspondences as in the figure below (red = input points, and blue = desired positions after transformation): <https://lh4.googleusercontent.com/-2SjXbAQwJHU/VGsi-bqv8OI/AAAAAAAABSw/Jsni…> Next I compute the transformation using skimage.transform.PolynomialTransform and a polynomial of order 2, and apply the transformation to get the warped image using skimage.transform.warp But the warped image is completely crazy! See below: <https://lh3.googleusercontent.com/-VZmvMqQjNTo/VGsjdSpuklI/AAAAAAAABS4/OsAH…> It seems the transformation found by PolynomialTransform is completely wrong... *Note that I managed to get a good transformation in some cases for sub-images (e.g using the first 400 columns only).* What am I doing wrong? Are PolynomialTransform too unstable? Do I need a regular grid? I attach the code I use (warp.py) Thanks for your help! Hervé

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Re: 3d blob detection
by Joel Bernier 02 Dec '14

02 Dec '14

Thanks Juan! On Wednesday, November 26, 2014 3:57:04 PM UTC-8, Juan Nunez-Iglesias wrote: > > Hi Joel, > > I'm the self-appointed Guardian of the of the Dimensions here at > scikit-image. =) This is a good idea and I will pop it near the top of the > list for conversion to 3D. Of course, pull requests are very welcome! If > you would like to try your hand at it, I'm happy to help you through any > hairy bits. =) > > Juan. > > On Thu, Nov 27, 2014 at 5:42 AM, Thomas Caswell <tcas...(a)gmail.com > <javascript:>> wrote: > >> It might be worth having a look at >> https://github.com/soft-matter/trackpy/pull/162 >> >> >> On Wed Nov 26 2014 at 1:34:54 PM Joel Bernier <joel.b...(a)gmail.com >> <javascript:>> wrote: >> >>> Any hope of modifying some of the tools in skimage.feature (say >>> blob_log() >>> <http://scikit-image.org/docs/dev/api/skimage.feature.html#skimage.feature.b…>) >>> to handle 3d images? I have a good application in the really of >>> processing X-rya diffraction data… >>> >>> -J >>> >>> -- >>> 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/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...(a)googlegroups.com <javascript:>. >> For more options, visit https://groups.google.com/d/optout. >> > >

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