Mailman 3 February 2014 - scikit-image

GitHub now does diffs on rendered prose
by Juan Nunez-Iglesias 14 Feb '14

14 Feb '14

Wow, it's like the entire universe is aligning to help us write this paper! =D https://github.com/blog/1784-rendered-prose-diffs

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Google Summer of Code 2014
by Stéfan van der Walt 13 Feb '14

13 Feb '14

Hi everyone If everything goes well, we'll be able to participate in this year's Google Summer of Code under the PSF umbrella. I've put up a page with ideas: https://github.com/scikit-image/scikit-image/wiki/GSoC-2014 Please have a look at it and edit as you see fit. Students, if you are interested in participating, now would be a great time to put in a few pull requests and to take part in conversations on the mailing list. Regards Stéfan

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io.Video hanging indefinitely on load
by !link 13 Feb '14

13 Feb '14

Hello, I'm trying to get skimage working with video, and I'm using a relatively small video to test the functionality I need. If I run the following code (with a video I know to play in multiple players) it seems to hang python. import os from skimage import io ** Message: pygobject_register_sinkfunc is deprecated (GstObject) video_path = os.path.join(os.getcwd(),'test.avi') data = io.Video(source = video_path) as in, I've let it run for 5 + min on a 2.5 MB file and had to kill the python process. I'm running OS X 10.9.1 and I have: Python 2.7.6 :: Anaconda 1.7.0 (x86_64) skimage 0.8.2 Gstreamer 1.2.3 from binary at http://gstreamer.freedesktop.org/ and gst-python010 installed In case it matters, I installed gst-python via: $ brew tap homebrew/versions $ brew install gst-python010 I would appreciate any suggestions or recommendations as to how to determine where the error is, and then how to go about correcting it.

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x,y coordinates of all the shape outlines
by Dan 11 Feb '14

11 Feb '14

Hi, I wish to get the x,y coordinates of all the shape outlines in this image http://break2012.weebly.com/uploads/1/3/5/8/13582971/682025_orig.gif Is it possible to do it using scikit-image? Thanks.

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Re: scikit-image paper
by Adam Hughes 11 Feb '14

11 Feb '14

Hey guys, I'm curious on your approach for introducing scikit image in the context of other available image processing libraries, without really stepping on anyone's toes so to speak. I'm referring to several image processing tools in a paper we're working on, and certainly would be interested in hearing your take on this issue. On Sun, Feb 9, 2014 at 6:37 PM, Juan Nunez-Iglesias <jni.soma(a)gmail.com>wrote: > Hi all, > > 1. I'm unsure about writing the education or industry sections of the > paper, as I have little experience in either. I'm currently working on > another research example. I think we can have two, since it's *sci*kit-image! > Who worked on the Novice module? They might be a good candidate for the > Education section. And Neil might be your man for industry... =) > > 2. For stitching, some electron microscopy tiled images are another > alternative, see e.g.: http://www.ini.uzh.ch/~acardona/trakem2_manual.html > > 3. Big fan of PeerJ so let's get this show started! =) > > Juan. > > > > On Mon, Feb 10, 2014 at 6:39 AM, Jérôme Kieffer <google(a)terre-adelie.org>wrote: > >> On Sun, 9 Feb 2014 19:47:06 +0200 >> Stéfan van der Walt <stefan(a)sun.ac.za> wrote: >> >> > On Sun, Feb 9, 2014 at 7:41 PM, Jérôme Kieffer <google(a)terre-adelie.org> >> wrote: >> > > I have plenty of panorama (already stitched) ... but raw images are >> > > available if you need for the publication. >> > > >> > > http://photo.terre-adelie.org/Panoramiques/html/dirindex.html >> > >> > That's awesome, thanks! We'll have a look through those and get in >> touch. >> > >> > Would it be acceptable to distribute the images freely with attribution? >> >> All those panorama (maybe there are 1 or 2 exceptions) have been >> assembled from images I took myself. I can specify a licence, probably >> CC-By it it fits you. Please take one without anybody on the image to >> avoid issues with what we call "droit à l'image" in French... (and >> doesn't exist in many counties: People appearing in content may have a >> right to control use of their image and to maintain their privacy.) >> http://fr.wikipedia.org/wiki/Droit_%C3%A0_l%27image >> >> Those panorama were assembled using gimp (before 2004) then with the help >> of >> Hugin. More recently I tested AutoPanoPro which is great while >> proprietary... >> >> Cheers, >> -- >> Jérôme Kieffer <google(a)terre-adelie.org> >> >> PS: I miss-used the word raw as they were all shout in JPEG mode. >> >> -- >> 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. >> > > -- > 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/ReKcHGSaATU/unsubscribe. > To unsubscribe from this group and all of its topics, 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: scikit-image paper
by Jérôme Kieffer 09 Feb '14

09 Feb '14

On Sun, 9 Feb 2014 19:47:06 +0200 Stéfan van der Walt <stefan(a)sun.ac.za> wrote: > On Sun, Feb 9, 2014 at 7:41 PM, Jérôme Kieffer <google(a)terre-adelie.org> wrote: > > I have plenty of panorama (already stitched) ... but raw images are > > available if you need for the publication. > > > > http://photo.terre-adelie.org/Panoramiques/html/dirindex.html > > That's awesome, thanks! We'll have a look through those and get in touch. > > Would it be acceptable to distribute the images freely with attribution? All those panorama (maybe there are 1 or 2 exceptions) have been assembled from images I took myself. I can specify a licence, probably CC-By it it fits you. Please take one without anybody on the image to avoid issues with what we call "droit à l'image" in French... (and doesn't exist in many counties: People appearing in content may have a right to control use of their image and to maintain their privacy.) http://fr.wikipedia.org/wiki/Droit_%C3%A0_l%27image Those panorama were assembled using gimp (before 2004) then with the help of Hugin. More recently I tested AutoPanoPro which is great while proprietary... Cheers, -- Jérôme Kieffer <google(a)terre-adelie.org> PS: I miss-used the word raw as they were all shout in JPEG mode.

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Re: incoherent face orientation in marching cubes
by Josh Warner 09 Feb '14

09 Feb '14

Calculate the gradient for each face, normalize it, and orient the face counterclockwise around the descent of said gradient vector. It would require some pretty heavy modification, but might be worth it. On the other hand, you could potentially hack in a fix (depends on how the STL package works) much easier by making the output double sided. A double-sided mesh has each face twice, covering both orientations This way you'd just append `faces` to itself, reverse indexing to flip the orientation of each face, e.g. ``` python import numpy as np from skimage.measure import marching_cubes verts, faces = marching_cubes(vol, value) faces = np.concatenate((faces, faces[:, -1], axis=0) # Remainder of STL export code for faces here ``` Which would be *far, far* simpler and less computationally intense than dealing with the gradients... Would you mind trying this quick fix, Janto? On Wednesday, January 8, 2014 6:35:28 PM UTC-6, Stefan van der Walt wrote: > > Josh, you said you had some ideas on how to add this--could you expand? >

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Re: scikit-image paper
by Johannes Schönberger 09 Feb '14

09 Feb '14

> This does look very appealing. I am sure we can hit that deadline > (Johannes is done with his section, mine is nearing completion and we > have two examples in the works). What other sections do we need? Introduction: Stefan Usage examples: Francois 1, Stefan 2 (?) Development practices: Johannes Roadmap: ??? (me?) Conclusion: (Stefan?)

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Re: Contribution to scikit-image
by Stéfan van der Walt 09 Feb '14

09 Feb '14

Hi Kakul On Sun, 09 Feb 2014 18:45:42 +0530, Kakul Chandra wrote: > I am a Computer Science undergraduate from Indian Institute of Technology > Roorkee. I am currently working on a project related to Text and Image > extraction from scanned Newspaper images.I am using scikit-image for that > purpose. I wanted to know I could contribute to scikit-image. We have a long list of bugs (some of them quite easy) that need to be fixed, so that would be one place to start. The other would be documentation. You can also look at our wiki at https://github.com/scikit-image/scikit-image in order to see a list of proposed future tasks. One feature I would like to see that is related to text is the stroke width transform. Regards StÃ©fan

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Contributing in Image Compression Algorithms
by MIT SHAH 09 Feb '14

09 Feb '14

Hi, I am working on Image Compression Algorithms. I want to contribute it in scikit-image. Can I contribute it ? I am asking this, because I didn't find Image Compression as Requested features on the following link : https://github.com/scikit-image/scikit-image/wiki/Requested-features Please guide me.

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