Mailman 3 February 2016 - scikit-image

Re: profile_line function
by Jaime Lopez Carvajal Feb. 23, 2016

Feb. 23, 2016

Hi Juan, I see your point, I read about the difference with Numpy indexing, but I did understand at that time. Your explanation is very clear, as well your suggestion about to use the shorter range. Thanks for your time. Jaime On Tuesday, February 23, 2016 at 6:15:31 PM UTC-5, Juan Nunez-Iglesias wrote: > > Hi Jaime, > > It's a bit confusing, but, because profile_line is used in interactive > tools, *the final point is included in the line*, unlike normal > Python/NumPy indexing. It would be unintuitive in interactive tools *not* > to include the final point. (This is in the "Notes" section in the > docstring.) So, your final point, (0, 10), is actually outside your image, > and the constant value of 0 is returned. I suspect that for your use case > you want to call profile_line(img, (0, 0), (0, 9)) and profile_line(img, > (0, 0), (9, 9)). I think it should work as expected in those cases. > > I hope that helps! > > Juan. > > On Wed, Feb 24, 2016 at 1:33 AM, Jaime Lopez Carvajal <jalo...(a)gmail.com > <javascript:>> wrote: > >> Hi, >> >> I would like to know why the function profile_line from profile.py in >> module skimage.measure, always return an additional value (zero value) at >> the end for horizontal and vertical lines, and two extra values (2 zeros) >> for diagonal lines. >> I mean, if I have an image 10x10, and I want the profile line >> >> > a = profile_line(img, (0, 0), (0, 10)) >> > array([ 83., 82., 81., 88., 95., 88., 93., 107., 121., >> 146., * 0.*]) >> >> and with diagonal lines it returns two additional values (2 zeros), like >> this: >> >> > a = profile_line(img, (0, 0), (10, 10)) >> > array([ 83., 92., 105., 123., 100., 69., 46., 46., 48., >> 52., 62., 70., 77., 84., *0., 0.*]) >> >> Thanks in advance for your comments, >> >> Jaime >> >> -- >> 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:>. >> To post to this group, send email to scikit...(a)googlegroups.com >> <javascript:>. >> To view this discussion on the web, visit >> https://groups.google.com/d/msgid/scikit-image/d4e6af4a-b4de-49b1-9e57-6391… >> <https://groups.google.com/d/msgid/scikit-image/d4e6af4a-b4de-49b1-9e57-6391…> >> . >> For more options, visit https://groups.google.com/d/optout. >> > >

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profile_line function
by Jaime Lopez Carvajal Feb. 23, 2016

Feb. 23, 2016

Hi, I would like to know why the function profile_line from profile.py in module skimage.measure, always return an additional value (zero value) at the end for horizontal and vertical lines, and two extra values (2 zeros) for diagonal lines. I mean, if I have an image 10x10, and I want the profile line > a = profile_line(img, (0, 0), (0, 10)) > array([ 83., 82., 81., 88., 95., 88., 93., 107., 121., 146., * 0.*]) and with diagonal lines it returns two additional values (2 zeros), like this: > a = profile_line(img, (0, 0), (10, 10)) > array([ 83., 92., 105., 123., 100., 69., 46., 46., 48., 52., 62., 70., 77., 84., *0., 0.*]) Thanks in advance for your comments, Jaime

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Re: 0.12 release
by Emmanuelle Gouillart Feb. 23, 2016

Feb. 23, 2016

Dear all, after having pressed everyone to finish pull requests and promised to take care of the release, I'm having a few busy days during which I can't find time to work on the release. It's going to be much better starting from Tuesday evening, so please bear with me and be patient: the release is (still) coming! And it means that there are still a few days to complete outstanding items on TODO.txt :-) Cheers, Emmanuelle On Wed, Feb 03, 2016 at 10:29:58AM -0800, StÃ©fan van der Walt wrote: > On 3 February 2016 at 09:21, Emmanuelle Gouillart > <emmanuelle.gouillart(a)nsup.org> wrote: > > Thanks for preventing us from being carried away by the excitement of the > > release :-D > Let me not stand in the way! I have three months' worth of happiness > pent up for the moment that tag gets applied. > Onward :) > StÃ©fan

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Livewire segmentation in scikit-image
by Pavlo Dyban Feb. 23, 2016

Feb. 23, 2016

Hello! I am a great fan of scikit-learn and have used it in a number of various projects so far. This time, I want to contribute to the project. I have implemented Livewire segmentation algorithm for image segmentation and would like to bring it into the main package. My code is hosted on github, it is documented with sphinx and tested. Livewire segmentation technique deduces object boundaries in the image by converting the image to a weighted graph where edges' weights are computed from the gradient image. The shortest path algorithm minimises the total cost function, thus avoiding steep gradients (i.e. object boundaries in the original image). An example of how the algorithm works you will find in my repository: https://github.com/pdyban/livewire. The API is straightforward: from livewire import LiveWireSegmentationalgorithm = LiveWireSegmentation(image)path = algorithm.compute_shortest_path((0, 0), (10, 25)) Do you think this algorithm would be needed inside scikit-image? If yes, would that belong inside segmentation module? Could someone assist me in my first open source contribution? It would be great if I could contribute to your project! Thanks!

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Scipy2016: call for proposals
by Nelle Varoquaux Feb. 22, 2016

Feb. 22, 2016

Dear all, SciPy 2016, the Fifteenth Annual Conference on Python in Science, takes place in Austin, TX on July, 11th to 17th. The conference features two days of tutorials by followed by three days of presentations, and concludes with two days of developer sprints on projects of interest to attendees. . The topics presented at SciPy are very diverse, with a focus on advanced software engineering and original uses of Python and its scientific libraries, either in theoretical or experimental research, from both academia and the industry. This year we are happy to announce two specialized tracks that run in parallel to the general conference (Data Science , High Performance Computing) and 8 mini-symposia (Earth and Space Science, Biology and Medicine, Engineering, Social Sciences, Special Purpose Databases, Case Studies in Industry, Education, Reproducibility) Submissions for talks and posters are welcome on our website ( http://scipy2016.scipy.org). In your abstract, please provide details on what Python tools are being employed, and how. The talk and poster submission deadline is March 25th, 2016, while the tutorial submission deadline is March, 21st, 2016. Important dates: Mar 21: Tutorial Proposals Due Mar 25: Talk and Poster Proposals Due May 11: Plotting Contest Submissions Due Apr 22: Tutorials Announced Apr 22: Financial Aid Submissions Due May 4: Talk and Posters Announced May 11: Financial Aid Recipients Notified May 22: Early Bird Registration Deadline Jul 11-12: SciPy 2016 Tutorials Jul 13-15: SciPy 2016 General Conference Jul 16-17: SciPy 2016 Sprints We look forward to an exciting conference and hope to see you in Austin in July! The Scipy 2016 http://scipy2016.scipy.org/ Conference Chairs: Aric Hagberg, Prabhu Ramachandran Tutorial Chairs: Justin Vincent, Ben Root Program Chair: Serge Rey, Nelle Varoquaux Proceeding Chairs: Sebastian Benthall

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Simple Docstring Improvements
by Austin Godber Feb. 18, 2016

Feb. 18, 2016

Hi All, I've just submitted the following simple pull request: https://github.com/scikit-image/scikit-image/pull/1948 It's a one line change to an example in the recttool docstring. I have found a few other like this, basically forgotten imports. I suppose it's possible these are deliberately omitted for some reason since some tend to fall into the category of "I didn't bother to show the import of the module this docstring documents". The question is, would you guys like me to fix these as I find them and if so would you prefer I batch them together in pull requests? Nice work with scikit image BTW. I am going through and learning more about the image viewer. Austin

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img_as_float
by Johannes Schönberger Feb. 18, 2016

Feb. 18, 2016

Hi everyone, There has been a little discussion in #1945 about our range conversion and I think that we should try to avoid `img_as_float` in our functions as much as possible, unless really necessary for the correctness of the algorithm. In most cases, there is no reason to tinker around with the range of values of the input image. Some examples: skimage.filter.gaussian_filter skimage.transform.warp et al. skimage.filter.sobel et al. skimage.restoration.denoise_tv_chambolle What is your opinion? Best, Johannes

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Gsoc 2016 - Project Ideas
by Vinay Chandragiri Feb. 17, 2016

Feb. 17, 2016

Hi All, This is Vinay. I am a senior undergrad majoring computer science from Indian Institute of Technology Guwahati and also a Computer Vision and Machine Learning enthusiast. I would like to contribute to scikit - image as a part of GSOC 2016. I faced the problem of Image Segmentation during one of my projects for neural images and I ended up using the below link, which was the best one available so far, in theory and in practice. http://fiji.sc/Morphological_Segmentation I personally think this plugin for scikit-image will be helpful to the community as most of them aren't aware of this as per my knowledge. What do you suggest ? I would like to hear your thoughts. Thanks, Vinay.

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Boundary/outline of objects in an Image
by ashz＠walla.co.il Feb. 15, 2016

Feb. 15, 2016

Hi, I try to focus on scikit-image instead of other non-open source software. Therefore, is there an example how to boundary/outline of objects in an Image? Something like this tutorial: http://www.mathworks.com/help/images/boundary-tracing-in-images.html Thanks

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linear texture
by Jaime Lopez Carvajal Feb. 15, 2016

Feb. 15, 2016

Hi all, I want to know if there exist some method to calculate texture using image lines from different sizes. I know that usually texture use square kernels (3x3, 5x5, etc), but I guess some years ago, I read about a method to obtain texture from lines. Any suggestion? Thanks, Jaime

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