Mailman 3 June 2015 - scikit-image

HOG feature extraction
by Manan Dey 25 Jun '15

25 Jun '15

Hi I want to extract HOG features from Handwritten Arabic Line Images. When I run the test_hog.py file from the scimage library from scikit. It runs without any errors but it doesnt print any features as output. Can anyone please help me how to print the features. The link to the program is https://code.google.com/p/pythonxy/source/browse/src/python/scikits.image/P…

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(Histogram?) plugin behaviour change?
by Nadav Horesh 22 Jun '15

22 Jun '15

Maybe there is a plugin behaviour change, since the color_histogram.py does not function as it used to, I suspect that for some reason the RectangleTool is attached to the image rather to the histogram window. I'd to have instructions how to fix it, since I've build a modification to ColorHistogram that it would be nice to fix. Thanks Nadav

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Enquiring about companies that rely on scikit-image
by Kevin Keraudren 21 Jun '15

21 Jun '15

Hi, I just came back from PyData London, which was a great experience. I thought I would see a bit more image processing outside of an academic context, but Lyst is the only one I noticed. I was surprised by the success of scikit-learn outside of academia [1], and I was wondering if people on the mailing list were aware of companies that would similarly rely on scikit-image? Kind Regards, Kevin [1] http://scikit-learn.org/stable/testimonials/testimonials.html

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Fwd: Your PeerJ article has been selected as one of our top bioinformatics papers
by François Boulogne 19 Jun '15

19 Jun '15

Dear all, The paper has been selected for the Top Bioinformatics Papers - June 2015. See the email of the editor below. Best. Fr. -------- Message transféré -------- Sujet : Your PeerJ article has been selected as one of our top bioinformatics papers Date : Fri, 19 Jun 2015 10:07:32 -0700 De : Peter Binfield <pete(a)peerj.com> Pour : boulogne(a)princeton.edu Dear François, On behalf of the PeerJ Team, I am writing to let you know that your PeerJ article (“/scikit-image: image processing in Python/” at https://peerj.com/articles/453/) has been named as one of our ‘top’ bioinformatics articles and is listed in our “Top Bioinformatics Papers - June 2015“ Collection. More information about this Collection is at: https://peerj.com/blog/post/115284878050/ and the Collection itself is at: https://peerj.com/collections/18-bioinf-062015/ Congratulations on this selection! We hope you consider PeerJ for your future publications. Yours Pete Binfield . . . Peter Binfield, PhD Co-Founder and Publisher, PeerJ Email: pete(a)PeerJ.com <mailto:pete@peerj.com> Web: PeerJ.com <https://peerj.com/> Twitter: @p_binfield <https://twitter.com/p_binfield>& @ThePeerJ <https://twitter.com/ThePeerJ> Blog: blog.PeerJ.com <http://blog.peerj.com/> Check out our new journal in Computer Science <https://peerj.com/computer-science/>

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Re: problem with measure.label
by Ji Zhou 17 Jun '15

17 Jun '15

Dear all, thanks for the help! I eventually figure out the issue is iPython Notebook is referring to a different skimage library, which was included in the Canopy distribution... import os path = os.path.dirname(skimage.__file__) /Users/zhouj/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/skimage So after uninstalling the Canopy distribution, it is working okay now :-) Cheers, Ji On Monday, 4 May 2015 16:46:09 UTC+1, Julien Derr wrote: > > Hi everyone, it is me again ... > I got this error with the label function > TypeError: label() got an unexpected keyword argument 'connectivity' > > but I used it exactly like written in the help : > > cc= label(binary2,connectivity=2) > > I thought it was maybe a problem of version, but it is written in my own > help when I type ?label, > so what could it be ? ideas? > > thanks again! > > Julien >

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Major and Minor axis length
by Anders Prier Lindvig 17 Jun '15

17 Jun '15

I have been using the scikit-image library for a segmentation task in my master thesis. More specifically I have used the regionprops function for calculation of major and minor axis length of objects. I was wondering why exactly, the eigenvalues are multiplied by 4, before returning the axis length? I realize that you multiply by 2 to get the full length, and I think you multiply by 2 again because of the standard deviation, but I am unsure about this.

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Re: problem with measure.label
by Josh Warner 13 Jun '15

13 Jun '15

This sounds like you may have conflicting Python installations. `conda` updating scikit-image successfully means you should have version 11.3 _somewhere_, but your PATH may still be preferentially finding a different Python/IPython different from the one your `conda` points to. Investigate this with `which python` to see what the system is doing when you ask for Python. Further instructions would probably best be obtained through the conda mailing list. On Saturday, June 13, 2015 at 3:37:56 PM UTC-5, Ji Zhou wrote: > > I use conda to update scikit image package on mac. However after undating > and restarting the kernel, the scikit image was still 0.10.1 on mac. > > Interestingly, on my Windows machine, the same procedure has successfully > update scikit image. > > One thing I shall point out is that I tried to uninstall anaconda on my > mac and was failed. > > Ji > On 13 Jun 2015 16:33, "Stefan van der Walt" <stefanv(a)berkeley.edu> wrote: > >> On 2015-06-13 06:50:03, Ji Zhou <gashjizhou(a)gmail.com> wrote: >> >>> I still cannot update the version of iPython notebook. Could you please >>> give me a hand? >>> >> >> What do you mean by this? Do you mean that you cannot access the latest >> version of skimage? You'll have to restart your notebook kernel. >> >> 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/-YegZib4VK8/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. >> >

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Re: problem with measure.label
by Ji Zhou 13 Jun '15

13 Jun '15

Dear all, Many thanks for the prompt response! I checked the version of scikit image, which suggests that it is 0.10.1. However, after I used conda install scikit-image=0.11.3 I still cannot update the version of iPython notebook. Could you please give me a hand? Cheers, Ji On Saturday, 13 June 2015 02:28:35 UTC+1, Juan Nunez-Iglesias wrote: > > This looks like a version problem. Connectivity was added in 0.11. > > On Sat, Jun 13, 2015 at 4:33 AM, Josh Warner <silvertr...(a)gmail.com > <javascript:>> wrote: > >> I cannot reproduce with everything installed fresh via miniconda on Win7. >> >> >>> from skimage.measure import label>>> import numpy as np>>> label(np.zeros(5), connectivity=1) >> array([0, 0, 0, 0, 0], dtype=int64) >> >> On Friday, June 12, 2015 at 12:20:43 PM UTC-5, stefanv wrote: >> >> On 2015-06-12 08:04:46, Ji Zhou <gashj...(a)gmail.com <javascript:>> >>> wrote: >>> > I have the same issue when using scikit image (Anaconda >>> > distribution, which is up-to-date) to label some image >>> > objects. Error messages are: >>> >>> Can you please verify your version? >>> >>> import skimage >>> print(skimage.__version__) >>> >>> Thanks >>> 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...(a)googlegroups.com <javascript:>. >> For more options, visit https://groups.google.com/d/optout. >> > >

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Re: problem with measure.label
by Ji Zhou 13 Jun '15

13 Jun '15

Hi, I have the same issue when using scikit image (Anaconda distribution, which is up-to-date) to label some image objects. Error messages are: from skimage.measure import label import numpy as np label(np.zeros(5), connectivity=1) ---------------------------------------------------------------------------TypeError Traceback (most recent call last)<ipython-input-2-df99425b8b1f> in <module>() 2 import numpy as np 3 ----> 4 label(np.zeros(5), connectivity=1) TypeError: label() got an unexpected keyword argument 'connectivity' Could you help? Ji On Monday, 4 May 2015 16:46:09 UTC+1, Julien Derr wrote: > > Hi everyone, it is me again ... > I got this error with the label function > TypeError: label() got an unexpected keyword argument 'connectivity' > > but I used it exactly like written in the help : > > cc= label(binary2,connectivity=2) > > I thought it was maybe a problem of version, but it is written in my own > help when I type ?label, > so what could it be ? ideas? > > thanks again! > > Julien >

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SciPy 2015 Birds-of-a-Feather Submission
by Matthew McCormick 11 Jun '15

11 Jun '15

Members of the scikit-image Community, As one of the co-chairs in charge of organizing the birds-of-a-feather sessions at SciPy this year, I wanted to reach out to your community to encourage you to submit a BoF proposal. A BoF session is an opportunity to open up a discussion on topics related to scikit-image development, future or just general questions. Please let us know if there is anything we can help with in terms of organization. More details can be found here: http://scipy2015.scipy.org/ehome/115969/259291/?& Kyle Mandli and Matt McCormick

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