Mailman 3 December 2013 - scikit-image

Close an image window?
by Alasdair McAndrew 19 Dec '13

19 Dec '13

This is a trivial question, but I still don't know how to do it. I've started up "ipython --pylab" and then: import skimage.io as io c = io.imread('cameraman.jpg') io.imshow(c,'qt') and this gives me an image in a window labelled "skimage". (I'm using Ubuntu 12.04). But how do I close this window from the console? I've tried: plt.close('skimage') plt.close() plt.close('all') plt.close(1) none of which have any effect. I can of course close them with the mouse, but that seems a little inelegant. Is the method to "close" the window in another package entirely? Thanks!

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slic segmentation
by scott.richardson＠visionsystemsinc.com 18 Dec '13

18 Dec '13

I recently upgraded skimage from release 0.8.2.0 to 0.9.3 and noticed that I am getting back a different segmentation than I used to. I see that @jni and @ahojnnes have made quite a few edits to skimage/segmentation/slic_superpixels.py and _slic.pyx, so I suspect that is expected, but I wanted to make sure it wasn't a regression. thanks Scott

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Re: Linking events in skimage.viewer
by Nadav Horesh 18 Dec '13

18 Dec '13

Thank you Juan. IIt looks like the event caught by the CanvasToolBase are not whtn I am looking for (mouse click and keyboard events) Thank you again, Nadav 2013/12/18 Juan Nunez-Iglesias <jni.soma(a)gmail.com>: > Hi Nadav, > > I don't have much experience with interactive tools, but I think this is the > right place to start for examples: > https://github.com/scikit-image/scikit-image/blob/master/skimage/viewer/can… > > You'll see that the LineProfile plugin uses the LineTool canvas tool: > https://github.com/scikit-image/scikit-image/blob/master/skimage/viewer/plu… > > Hopefully this helps, otherwise @tonysyu might be able to step in and offer > a bit more guidance. > > Juan. > > > > > On Wed, Dec 18, 2013 at 7:13 PM, Nadav Horesh <nadavh.horesh(a)gmail.com> > wrote: >> >> I >> I started to build an interactive image exploration utility based on >> matplotlib. Recently, following a link on this list, I encountered >> skimage.viewer, and found that the plugins architecture matches my needs. >> I could not find how to link keyboard and mouse events (and maybe buttons) >> to plugins. Any suggestions? >> >> I am using version 0.93 on linux (I can install the pre 0.10, if needed) >> >> Thanks, >> >> Nadav >> >> -- >> 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 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.

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Re: Linking events in skimage.viewer
by Juan Nunez-Iglesias 18 Dec '13

18 Dec '13

Hi Nadav, I don't have much experience with interactive tools, but I think this is the right place to start for examples: https://github.com/scikit-image/scikit-image/blob/master/skimage/viewer/can… You'll see that the LineProfile plugin uses the LineTool canvas tool: https://github.com/scikit-image/scikit-image/blob/master/skimage/viewer/plu… Hopefully this helps, otherwise @tonysyu might be able to step in and offer a bit more guidance. Juan. On Wed, Dec 18, 2013 at 7:13 PM, Nadav Horesh <nadavh.horesh(a)gmail.com>wrote: > I > I started to build an interactive image exploration utility based on > matplotlib. Recently, following a link on this list, I encountered > skimage.viewer, and found that the plugins architecture matches my needs. > I could not find how to link keyboard and mouse events (and maybe buttons) > to plugins. Any suggestions? > > I am using version 0.93 on linux (I can install the pre 0.10, if needed) > > Thanks, > > Nadav > > -- > 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. >

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Linking events in skimage.viewer
by Nadav Horesh 18 Dec '13

18 Dec '13

I I started to build an interactive image exploration utility based on matplotlib. Recently, following a link on this list, I encountered skimage.viewer, and found that the plugins architecture matches my needs. I could not find how to link keyboard and mouse events (and maybe buttons) to plugins. Any suggestions? I am using version 0.93 on linux (I can install the pre 0.10, if needed) Thanks, Nadav

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Re: Interactive selection of markers/seeds for random walk
by Kevin Keraudren 17 Dec '13

17 Dec '13

Hi, What about skimage.viewer.plugins.labelplugin.LabelPainter, there is an example with the watershed algorithm there: https://github.com/scikit-image/scikit-image/blob/master/viewer_examples/pl… Otherwise, with OpenCV, you could look at the GrabCut example: https://github.com/Itseez/opencv/blob/master/samples/python2/grabcut.py Kind regards, Kevin On Mon, Dec 16, 2013 at 7:08 PM, Adam Hughes <hughesadam87(a)gmail.com> wrote: > Hi, > > I was wondering if anyone had any examples or tools that would allow one > to interactively select regions for seeds/markers in an image, which we > could subsequently run the randomwalk algorithm over: > > > http://scikit-image.org/docs/dev/auto_examples/plot_random_walker_segmentat… > > I really enjoyed the ilastik tool that scikit image lists under its > related links on the homepage, and wondered if there were any demos for > selection that might be easily adaptable to fit this purpose. > > Thanks! > > -- > 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. >

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Re: New examples
by Stéfan van der Walt 16 Dec '13

16 Dec '13

On Sun, Dec 15, 2013 at 10:18 PM, Adam Hughes <hughesadam87(a)gmail.com> wrote: > Actually, it looks like the user guide already has a nice section that might > be the right place for this: > > http://scikit-image.org/docs/0.9.x/user_guide/getting_help.html Another option would be to have a "side scrolling" bar on the top of the gallery. I.e., we take about 300 pixels at the top to show the videos, the rest of the page loads the examples. If that's too complicated, simply linking to the place you mention would be ok. Stéfan

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Re: New examples
by Adam Hughes 16 Dec '13

16 Dec '13

Hey Stefan, I would be happy to try :) I'm confident I can gather the videos and stack overflow posts, but do you have a sense of where you'd like this information to fit into the website? In particular, I was thinking it could have either its own category (let's just call it "Outreach" at the moment) at this level: http://scikit-image.org/docs/0.9.x/ Or to lump it into the User Guide section, something like: User Guide: -section 1 -subsection - ... Community: - Video tutorials - Stack overflow posts Of course, it could also be bumped down directly into the User Guide: User Guide: -section1 -subsection -... - Outreach -video tutorials -stack overflow -mailing list discussions -more user examples I'm thinking user examples would be special links to repos or .ipynb files that aren't on the front page, but are often passed around on the mailing list. Any feelings about the organization Stefan? On Friday, December 13, 2013 9:34:38 PM UTC-5, Stefan van der Walt wrote: > > Hey, Adam > > On Sat, Dec 14, 2013 at 2:42 AM, Adam Hughes <hughes...(a)gmail.com<javascript:>> > wrote: > > Perhaps put any videos like this in the gallery as well? > > We could also add links to StackOverflow posts. > > Would you mind being our curator, and send a pull request either on > the website repo or on the docs to make this happen? > > Thank you! > Stéfan >

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Interactive selection of markers/seeds for random walk
by Adam Hughes 16 Dec '13

16 Dec '13

Hi, I was wondering if anyone had any examples or tools that would allow one to interactively select regions for seeds/markers in an image, which we could subsequently run the randomwalk algorithm over: http://scikit-image.org/docs/dev/auto_examples/plot_random_walker_segmentat… I really enjoyed the ilastik tool that scikit image lists under its related links on the homepage, and wondered if there were any demos for selection that might be easily adaptable to fit this purpose. Thanks!

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Re: Restoration module
by Johannes Schönberger 14 Dec '13

14 Dec '13

Great contribution! Are there any other "filters" that should go into this new sub-package? Johannes Am 14.12.2013 um 04:07 schrieb Stéfan van der Walt <stefan(a)sun.ac.za>: > Hi everyone, > > Just a heads-up on a new scikit-image submodule: ``skimage.restoration``. > > Thanks to François Orieux, we are fortunate to have the following > deconvolution algorithms implemented: > > [1] `wiener` > [2] `unsupervised_wiener` > [3] `richardson_lucy` > > I'd pay specific attention to Francois' own algorithm [2] -- no more > painful parameter tweaking to get a good Wiener-Hunt deconvolution! > > Thanks also to everyone on the team who worked hard to review and shape this PR. > > 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.

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