scikit-image April 2011

scikit-image@python.org

11 participants
17 discussions

Re: Re : Re: convex hull of a 2D binary image
by Chris Colbert 21 Apr '11

21 Apr '11

So, there are a couple of ways you could do that. One is by using structuring elements as indicated in G & W. Another way would be to take a 3D method like described here in the surface approximation section (shameless plug): http://confactsdatas.inrialpes.fr/IEEE_RSJ_-_IROS_2010_International_Confer… and adapt it for 2D. There is nothing in scikits.image that will do this automatically, but it would be a useful feature so I'll add it to my TODO list. Chris On Wed, Apr 20, 2011 at 12:00 PM, jip <jeanpatrick.pommier(a)gmail.com> wrote: > no, just the convex hull of a a 2D image. > I found the definition in "Gonzalez & Woods, p545", but I am not sure to > implement the stuff. > > jean-patrick >

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Re: Re : Re: Re : Re: How to get an ordered list of coordinates of a curve?
by Pieter Holtzhausen 21 Apr '11

21 Apr '11

https://code.ros.org/trac/opencv/browser/trunk/opencv/samples/python/cv20sq… Check the examples...they serve as a good guide. On Wed, Apr 20, 2011 at 9:18 PM, jip <jeanpatrick.pommier(a)gmail.com> wrote: > Hi again > On my ubuntu box, I have: > > In [23]: from opencv.imgproc import FindContours > ------------------------------------------------------------ > Traceback (most recent call last): > File "<ipython console>", line 1, in <module> > ImportError: No module named imgproc > > Anyway, thank you for help > Best regards > > Jean-Patrick >

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Registration algorithms
by Stéfan van der Walt 20 Apr '11

20 Apr '11

Hi all, I noticed a recent publication in IEEE Transactions on Image Processing today: HAIRIS: A Method for Automatic Image Registration Through Histogram-Based Image Segmentation Hernâni Gonçalves, José Alberto Gonçalves, and Luís Corte-Real, Member, IEEE This could be a fun project! It seems to be a fairly robust method for doing registration without any tweaking parameters. I've also considered some other registration algorithms based on projections of the log-polar transform, in addition to existing code I wrote to do feature-based registration. Registration is one of the few "solved problems" that always causes problems! If you have bored students over the holidays, send them my way... Regards Stéfan

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Re: Re : Re: How to get an ordered list of coordinates of a curve?
by Chris Colbert 20 Apr '11

20 Apr '11

I don't use the official opencv bindings, but looking at their documentation: http://opencv.willowgarage.com/documentation/python/index.html It looks like it may live at opencv.imgproc.FindContours try: from opencv.imgproc import FindContours Otherwise, take the question to the opencv mailing list. On Wed, Apr 20, 2011 at 1:21 PM, jip <jeanpatrick.pommier(a)gmail.com> wrote: > unfortunately, FindContours is not in scikits.image. > > with opencv, there is somothing that I don't understand, I get: > > In [21]: import opencv > > In [22]: opencv.FindContours(...) > ------------------------------------------------------------ > Traceback (most recent call last): > File "<ipython console>", line 1, in <module> > AttributeError: 'module' object has no attribute 'FindContours' > > > I understand this is not an opencv group, but if you know how to solve that > issue ... > > Thank you > Jean-Patrick > >

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How to get an ordered list of coordinates of a curve?
by jip 20 Apr '11

20 Apr '11

Hi, Given a 2D image of a closed or open curve, as the outline of a binary particle or a skeleton,I am wondering how to get an order list of the pixels coordinates (I found something in the opencv documentation <http://opencv.willowgarage.com/documentation/python/imgproc_structural_anal…>, but I am unable to call fincontours from python. For som reasons, I write import opencv then if I try opencv.findcontour, findcontour is not available in the list of my python ide<https://picasaweb.google.com/100950875858888510591/Spyder#55914059068626203…>( spyder <http://packages.python.org/spyder/>); I hope I am clear ) Thanks for your advice. Jean-Patrick

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convex hull of a 2D binary image
by jip 20 Apr '11

20 Apr '11

Hi, Does scikits.image provide a way to compute the convex hull of a binary image? Something like : cHull=convexhull(binary_image) thank you Jean-Patrick

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Sobel / Prewitt Edge Detection
by Stéfan van der Walt 20 Apr '11

20 Apr '11

Hi all, Pieter Holtzhausen made a pull request to bring over the Sobel / Prewitt edge detection filters from CellProfiler. I reviewed and merged his code, alongside with the connected components changes suggested last week. You can find the changesets here: https://github.com/stefanv/scikits.image/commit/cef53c172dd3e15dc98ddbf97a9… Please review and comment--you input is highly valued! Regards Stéfan

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Re: Help needed using pymorph
by Thouis (Ray) Jones 13 Apr '11

13 Apr '11

(Note, I'm responding to both pythonvision and scikits-image. Sorry to those people only subscribed to one list.) I think more information might be helpful. - How many images do you have that you need to analze? - Are they movies, or completely separate frames? - What is common in the images (background, lighting, camera pose?) I wouldn't worry about efficient multi-template matching until you know if multi-template matching works at all. If template matching can get 60% of the beads, though, I expect multiple templates should be able to get almost all of them, possibly using a voting scheme where you require a bead to match multiple different templates before reporting it as a "hit". You might look at ilastik (http://www.ilastik.org/) as another approach. Thouis Jones On Tue, Apr 12, 2011 at 06:24, Alex Liberzon <alex.liberzon(a)gmail.com> wrote: > Thanks for the feedback. > > There are both effects, the beads are different sizes and also as you > noticed at different depths. but the variation is not very large, i.e. > within a difference of 10 - 15 pixels I'd say. I have no idea how to > use multiple templates efficiently. Of course I can repeat normalized > cross correlation attempt few times. > > I can modify the experiment, so the next time will be hopefully > better. Meanwhile, this data is important to extract from the images > as is. > > Regards, > Alex > > On Apr 11, 10:56 pm, "Thouis (Ray) Jones" <tho...(a)gmail.com> wrote: >> Are the beads actually different sizes, or just at different depths in >> the image. And how fixed is your camera system relative to the scene? >> I ask, because it seems like you could use multiple templates, >> parameterized by image position, to adjust for the size and blur >> variation. >> >> Also, do you have the option of modifying the scene illumination? Can >> you use color, or multiple exposures, or are the images "as-is" and >> there's no option for making the beads more visible? >> >> Best, >> Ray Jones >> >> >> >> On Mon, Apr 11, 2011 at 19:49, Alex Liberzon <alex.liber...(a)gmail.com> wrote: >> > Dear pymorph members, >> >> > I have some difficulty to identify specific objects from the grayscale >> > image. For example, in this image >> >https://picasaweb.google.com/lh/photo/FYZ1_F4OAoe920iYj8bk7A?feat=dir... >> > one can see about 15 glass beads on the floor illuminated from the >> > left side. Human eye identifies them easily, but I cannot find the >> > efficient way to identify them in such an image. Using Matlab the >> > approach was 1) crop out one of the beads as is from the given image, >> > and then 2)using normalized cross-correlation (normxcorr2) of the >> > cropped bead with the image to identify the 50 - 60% of beads. The >> > problems are due to uneven background illumination, different size of >> > the beads and different light pattern due to their angle in respect to >> > the light source. >> > I could define the the problem of looking a feature that has two not- >> > connected bright regions, separated by some distance that could be >> > known within some reasonable limits. >> >> > Any suggestion is gratefully appreciated. If possible, the pseudo-code >> > would be helpful. Note that I also posted this question on skikits- >> > image mailing list so if you receive it double, I apologize for that. >> >> > Thanks, >> > Alex

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Re: "sudo easy_install scikits.image" fails
by Stéfan van der Walt 13 Apr '11

13 Apr '11

On Wed, Apr 13, 2011 at 10:46 AM, jip <jeanpatrick.pommier(a)gmail.com> wrote: > cython -V > Cython version 0.12.1 This would be the problem; you need version 0.13 or later to compile the latest Git version of the scikit. Cheers Stéfan

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Re: "sudo easy_install scikits.image" fails
by Stéfan van der Walt 13 Apr '11

13 Apr '11

On Wed, Apr 13, 2011 at 8:56 AM, jip <jeanpatrick.pommier(a)gmail.com> wrote: > creating build/temp.linux-i686-2.6 > compile options: '-I/usr/lib/python2.6/dist-packages/numpy/core/ > include -I/usr/lib/python2.6/dist-packages/numpy/core/include -I/usr/ > include/python2.6 -c' > gcc: opencv_backend.c > gcc: opencv_backend.c: Aucun fichier ou dossier de ce type Looks like it can't find the .c files. Can you provide the output of the "cython -v" command, please? I can chat to you on irc or gtalk, if that would help to resolve the issue more quickly. Regards Stéfan

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scikit-image April 2011