Mailman 3 February 2013 - scikit-image

Re: removing small connected components
by Juan Nunez-Iglesias Feb. 11, 2013

Feb. 11, 2013

Ah, academia, where the fun never stops! =) I will both submit this PR and review a few. Thanks for getting back to me! On Sat, Feb 9, 2013 at 4:31 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > :) I think this would a great addition. I think the only reason you have > heard anything thus far is that the core devs are pretty busy with other > things. We could always use more core devs, so if you (or anyone else out > there) want to review some PRs, I don't think it'd take long for you get > commit rights. > > Unfortunately, I'm also pretty busy these days, so no promises from me of > reviewing any PRs in the near future. ;) > > -Tony > > On Wed, Feb 6, 2013 at 7:10 AM, Juan Nunez-Iglesias <jni.soma(a)gmail.com>wrote: > >> Anyone? Bueller? Bueller? =) >> >> >> On Thu, Jan 31, 2013 at 2:19 PM, Juan Nunez-Iglesias <jni.soma(a)gmail.com>wrote: >> >>> Hi guys, >>> >>> For my own segmentation package, I wrote a small function to remove >>> small connected components in an ndarray. You can see it here: >>> >>> https://github.com/janelia-flyem/gala/blob/master/gala/morpho.py#L72 >>> >>> I've been looking at things that could be moved from there to skimage >>> and I thought that was a prime candidate (I think you actually do the same >>> thing in one of the examples, but without making it into a function). Any >>> interest in a PR? >>> >>> There's other nd operations in there: morphological reconstruction, >>> h-minima, regional (aka local) minima, and impose minima. Let me know if >>> you would like any of these for inclusion in skimage... >>> >>> Thanks, >>> >>> Juan. >>> >> >> -- >> 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: removing small connected components
by Tony Yu Feb. 9, 2013

Feb. 9, 2013

:) I think this would a great addition. I think the only reason you have heard anything thus far is that the core devs are pretty busy with other things. We could always use more core devs, so if you (or anyone else out there) want to review some PRs, I don't think it'd take long for you get commit rights. Unfortunately, I'm also pretty busy these days, so no promises from me of reviewing any PRs in the near future. ;) -Tony On Wed, Feb 6, 2013 at 7:10 AM, Juan Nunez-Iglesias <jni.soma(a)gmail.com>wrote: > Anyone? Bueller? Bueller? =) > > > On Thu, Jan 31, 2013 at 2:19 PM, Juan Nunez-Iglesias <jni.soma(a)gmail.com>wrote: > >> Hi guys, >> >> For my own segmentation package, I wrote a small function to remove small >> connected components in an ndarray. You can see it here: >> >> https://github.com/janelia-flyem/gala/blob/master/gala/morpho.py#L72 >> >> I've been looking at things that could be moved from there to skimage and >> I thought that was a prime candidate (I think you actually do the same >> thing in one of the examples, but without making it into a function). Any >> interest in a PR? >> >> There's other nd operations in there: morphological reconstruction, >> h-minima, regional (aka local) minima, and impose minima. Let me know if >> you would like any of these for inclusion in skimage... >> >> Thanks, >> >> Juan. >> > > -- > 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: removing small connected components
by Juan Nunez-Iglesias Feb. 6, 2013

Feb. 6, 2013

Anyone? Bueller? Bueller? =) On Thu, Jan 31, 2013 at 2:19 PM, Juan Nunez-Iglesias <jni.soma(a)gmail.com>wrote: > Hi guys, > > For my own segmentation package, I wrote a small function to remove small > connected components in an ndarray. You can see it here: > > https://github.com/janelia-flyem/gala/blob/master/gala/morpho.py#L72 > > I've been looking at things that could be moved from there to skimage and > I thought that was a prime candidate (I think you actually do the same > thing in one of the examples, but without making it into a function). Any > interest in a PR? > > There's other nd operations in there: morphological reconstruction, > h-minima, regional (aka local) minima, and impose minima. Let me know if > you would like any of these for inclusion in skimage... > > Thanks, > > Juan. >

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Re: Citing scikit-image
by Stéfan van der Walt Feb. 6, 2013

Feb. 6, 2013

Dear Stuart On Tue, Feb 5, 2013 at 3:55 PM, Stuart Mumford <littlemumford(a)gmail.com> wrote: > Do you have a preferred citation for scikit-image? It has been very handy > for me!! That's wonderful to hear! Unfortunately, we have no publications as of yet (although, you would receive the much adoration from the developers should you decide to write one :-). For now, if you could simply cite the website, and please let us know once it's been published (perhaps we can put a list of skimage publications on the website?). Stéfan

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Re: Vertical wraparound on MCP
by Stéfan van der Walt Feb. 5, 2013

Feb. 5, 2013

Dear Laurens On Tue, Feb 5, 2013 at 6:31 AM, Laurens Leerink <laurens.leerink(a)gmail.com> wrote: > One doesn't want to add too many (application specific) arguments to an elegant design, but has anyone proposed/requested a vertical wraparound option on the MCP costs array? (just to clarify, the idea is to connect the first and last rows of the costs array) I can certainly see many uses for this--the only concern would be if it makes the code much less readable, or if it slows down the algorithm significantly. If you want to submit a PR we'll gladly review it. Stéfan

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Re: Release plan for 0.8
by Schönberger Johannes Feb. 4, 2013

Feb. 4, 2013

I think we should push the release some days back to fix the majority of these issues. > https://github.com/scikit-image/scikit-image/issues/318 I'll take on this tomorrow. > https://github.com/scikit-image/scikit-image/issues/336 Made the necessary changes today as part of a new PR. > https://github.com/scikit-image/scikit-image/issues/341 I commented on this topic on github. > https://github.com/scikit-image/scikit-image/issues/418 (check relevance) Has been fixed before, so closed.

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Re: Contribution: circles and hough transform
by Stéfan van der Walt Feb. 3, 2013

Feb. 3, 2013

Hi François Yes, you may rely on Cython, so no need to code a pure Python version. Renaming the function as suggested would break backward compatibility, so I suggest adding hough_line as an alias, and deprecating hough over two releases. Regards Stéfan On Feb 3, 2013 9:04 PM, "François" <francois.boulogne(a)gmail.com> wrote: Hi, I have written the hough transform for circles in python and have a good basis for peak detection. I have few questions: 1/ in skimage/transform/hough_transform.py Cython version of hough() is imported like this (below the python version) 59 # try to import and use the faster Cython version if it exists 60 try: 61 from ._hough_transform import _hough 62 except ImportError: 63 pass Should I do the same for hough_circle()? or just implement the cython version? I don't see why cython would not be available... 2/ For disambiguation, I suggest to rename hough to hough_line(). The same for peak detection. Any comment on that? Cheers, François. <https://fr.wiktionary.org/wiki/disambiguation#en><https://fr.wiktionary.org/wiki/disambiguation#en> -- 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: Contribution: circles and hough transform
by François Feb. 3, 2013

Feb. 3, 2013

Le mercredi 9 janvier 2013 17:05:53 UTC+1, Stefan van der Walt a écrit : > > > Both patches would be very welcome! Let us know if you need any help > getting started. > > Thank. I discovered in master circle_perimeter(). This is actually the bresenham method. This PR is for Andres method. https://github.com/scikit-image/scikit-image/pull/410 Since bresenham in already in master, I'm working on the hough transform. :) François.

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Re: Displaying video
by Colin Lea Feb. 1, 2013

Feb. 1, 2013

Great. Thanks to both of you. I have implemented a video viewer using visvis that works very similarly to opencv (including registering key presses). I'll submit a PR in the next couple of days to see if anyone is interested in including it in skimage. On Friday, February 1, 2013 2:36:26 AM UTC-5, Otto wrote: > > I used WX to display frames from a video within my GUIs, it works well: > > > http://wxpython.org/docs/api/wx.DC-class.html > > > 2013/2/1 Almar Klein <almar...(a)gmail.com <javascript:>> > >> You could do it with OpenGl, although it wouldn't be straightforward. You >> can also do it in visvis (which uses OpenGl). Here's some untested code >> that would do this: >> >> import visvis as vv >> vv.clf() # Clear figure (or create a new figure) >> tex = vv.imshow(first_frame) >> >> while video_not_ended: >> tex.SetData(next_frame) >> time.sleep(1.0/framerate) >> vv.processEvents() >> >> - Almar >> >> >> On 30 January 2013 22:07, Colin Lea <coli...(a)gmail.com <javascript:>>wrote: >> >>> For a long time now I've kept OpenCV in my vision stack primarily for >>> displaying videos. I'm trying to get rid of it as a dependence for use on a >>> secure remote server which I don't have unfettered access to. >>> >>> So I'm wondering, how do other people display videos? I see that PyGame >>> is another option. Does anyone use that? By displaying videos essentially I >>> just mean showing streams of images (not necessary from a video file). >>> >>> If nobody else has a solution other than to use OpenCV, would it be of >>> interest to implement something (either using PyGame or otherwise) for >>> skimage? >>> >>> >>> -- >>> 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/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...(a)googlegroups.com <javascript:>. >> For more options, visit https://groups.google.com/groups/opt_out. >> >> >> > >

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Re: Displaying video
by Otto Fajardo Feb. 1, 2013

Feb. 1, 2013

I used WX to display frames from a video within my GUIs, it works well: http://wxpython.org/docs/api/wx.DC-class.html 2013/2/1 Almar Klein <almar.klein(a)gmail.com> > You could do it with OpenGl, although it wouldn't be straightforward. You > can also do it in visvis (which uses OpenGl). Here's some untested code > that would do this: > > import visvis as vv > vv.clf() # Clear figure (or create a new figure) > tex = vv.imshow(first_frame) > > while video_not_ended: > tex.SetData(next_frame) > time.sleep(1.0/framerate) > vv.processEvents() > > - Almar > > > On 30 January 2013 22:07, Colin Lea <colincsl(a)gmail.com> wrote: > >> For a long time now I've kept OpenCV in my vision stack primarily for >> displaying videos. I'm trying to get rid of it as a dependence for use on a >> secure remote server which I don't have unfettered access to. >> >> So I'm wondering, how do other people display videos? I see that PyGame >> is another option. Does anyone use that? By displaying videos essentially I >> just mean showing streams of images (not necessary from a video file). >> >> If nobody else has a solution other than to use OpenCV, would it be of >> interest to implement something (either using PyGame or otherwise) for >> skimage? >> >> >> -- >> 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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