Mailman 3 February 2017 - scikit-image

Squash merges
by Stefan van der Walt 17 Feb '17

17 Feb '17

Core team, I have re-enabled the squash merge button. I still think, ideally, that contributors should organize their patches as best they can, but at the same time this is a convenient way of merging simple changes that had to go through a few commit iterations. Please use as you see fit. Thanks Stéfan

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Announcing: Docathon, week of 6 March 2017
by Stefan van der Walt 17 Feb '17

17 Feb '17

Hi everyone, Please see the announcement below for a docathon to be held at BIDS in March. You do not need to be on campus to contribute. I hope to make some progress on the scikit-image docs, specifically by including examples of how to interact with other tools (ImageJ, Keras, etc.) and how to do some common tasks (like painting a mask in Gimp). I hope you can join us. Best regards Stéfan *What's a Docathon?* It's a week-long sprint where we focus our efforts on improving the state of documentation in the open-source and open- science world. This means writing better documentation, building tools, and sharing skills. *Who’s this for?* Anyone who is interested in improving the understandability, accessibility, and clarity of software! This might mean developers with a particular project, or individuals who would like to contribute to a project. You don’t need to use a specific language (though there will be many Python and R developers) and you don’t need to be a core developer in order to help out. *Where can I sign up?* Check out the _Docathon website_[1]. You can sign up as a _participant_[2], _suggest a project_[3] to work on, or sign up _to host your own_[4] remote Docathon wherever you like. You don’t have to use a specific language - we’ll be as accommodating as possible! *When is the Docathon?* The Docathon will be held *March 6 through March 10*. For those coming to BIDS at UC Berkeley, on the first day we'll have tutorials about documentation and demos of documentation tools, followed by a few hours of hacking. During the middle of the week, we'll set aside a few hours each afternoon for hacking as a group at BIDS. On the last day, we'll have a wrap-up event to show off what everybody worked on. *Where will the Docathon take place?* There are a _few docathons being held simultaneously_[5], each with their own schedule. At Berkeley we'll have a physical presence at BIDS over the week, and we encourage you to show up for the hours we set aside for doc hacking. However, it is totally fine to work remotely; we will coordinate people via email/GitHub, too. *Where can I get more information?* Check out an updated schedule, list of tutorials, and more information at our website here: _bids.github.io/docathon_. *Contact* If you have any questions, open an issue on our _GitHub repo_[6]. We look forward to hearing from you! Please feel free to forward this email to anyone who may be interested. We'd love for other institutions/groups to get involved. Links: 1. https://bids.github.io/docathon/ 2. https://goo.gl/forms/AaW2b24mMxOutxt02 3. https://goo.gl/forms/0cPpw01zehrEyDDE3 4. https://bids.github.io/docathon/pages/hosting.html 5. https://bids.github.io/docathon/pages/hosts.html 6. https://github.com/BIDS/docathon

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Re: [scikit-image] Introductory shoutout
by Steven Silvester 16 Feb '17

16 Feb '17

Hello Soumya and Vibhuti, and welcome! Regards, Steve > On Feb 15, 2017, at 12:58 PM, Soumya Gupta <soumyag213(a)gmail.com> wrote: > > Hello, > > My teammate (Vibhuti) and I are excited at the prospect of working with scikit-image especially for RGSOC. We're interested in Image Processing and Computer Vision. We're adept at Python, but novices in Image Processing and CV. We've done courses in college detailed on programming, algebra and calculus. > > We're pursuing a project on signal processing with EEG signals parallely, and we're hoping that this knowledge complements that of scikit-image. We'll be taking up the issues tagged with the novice tag. > We'll comparatively new to the open-source community, so we might be a bother while settling in. > > Looking forward to lots of contributions! > > > Best, > Soumya Atul Gupta > Final Year Undergraduate Student, ECE > Netaji Subhas Institute of Technology > New Delhi, India > > _______________________________________________ > scikit-image mailing list > scikit-image(a)python.org > https://mail.python.org/mailman/listinfo/scikit-image

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Introductory shoutout
by Soumya Gupta 16 Feb '17

16 Feb '17

Hello, My teammate (Vibhuti) and I are excited at the prospect of working with scikit-image especially for RGSOC. We're interested in Image Processing and Computer Vision. We're adept at Python, but novices in Image Processing and CV. We've done courses in college detailed on programming, algebra and calculus. We're pursuing a project on signal processing with EEG signals parallely, and we're hoping that this knowledge complements that of scikit-image. We'll be taking up the issues tagged with the novice tag. We'll comparatively new to the open-source community, so we might be a bother while settling in. Looking forward to lots of contributions! Best, Soumya Atul Gupta Final Year Undergraduate Student, ECE Netaji Subhas Institute of Technology New Delhi, India

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Do we trust image measurements?
by Stefan van der Walt 14 Feb '17

14 Feb '17

Hi, everyone This paper was recently published at IEEE Big Data: http://ieeexplore.ieee.org/abstract/document/7840755/ [0] It evaluates scikit-image, ImageJ, and other packages for accuracy. I've contacted the authors in the hope of getting more frequent access to their system (or their suite of tests), so that we can calibrate our accuracy a-la ASV (https://github.com/spacetelescope/asv). Stéfan [0] "The paper addresses the problem of understanding quality of image measurements extracted using widely used software libraries from large images. Image measurements (features) are extracted using software packages that vary in terms of programming languages, theoretical formulas for the same image feature, algorithmic implementations, input parameters, units of measurements, and definitions of image regions of interest. Our motivation is to quantify numerical variability of image features across software packages and determine image accuracy with respect to reference images. In addition, our objective is to enable scientists to extract any image features of interest from heterogeneous software libraries and gain provenance of every extracted numerical feature value. The provenance information is critical to achieve traceability of computations in terascale imaging. We pursue this objective by designing a client-server system that integrates image feature extractions from open source libraries such as ImageJ/Fiji, Python (scikit-image), CellProfiler, and in-house Java software packages. The system becomes useful for evaluating quality of image measurements, leveraging distributed computational resources for feature computations over big image data, sharing resulting feature values, and reproducing the feature values based on provenance. As an application of the designed system, we report the quality evaluations of 319 image features extracted using ImageJ/Fiji, Python (scikit-image), CellProfiler and in-house Java software packages with 43 duplicate features across the four packages. Using the normalized difference as metric, we identified 6 out of the 43 common features to differ over 1% in value and discuss the sources of these numerical differences."

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Re: [scikit-image] RGSoC project : scikit-image
by Steven Silvester 14 Feb '17

14 Feb '17

Hi Ramya, I’d think contributing to scikit-image is a good way to learn image analysis and computer vision. You can start with a smaller self-contained change to learn the process, and then move on to more advanced topics. You can learn by first playing with one of our examples, and then writing one of your own. You can write another test case for an existing set of tests. You can read a paper with an interesting image processing technique, and then prototype it in Python. You can update existing documentation that might be confusing at first to read. We’d be happy to have your help! Regards, Steve > On Feb 13, 2017, at 8:58 AM, Ramya Y S <yellapragada15117(a)iiitd.ac.in> wrote: > > Hey > > We (my teammate, Akarsha is cc'ed ) are interested in Image Analysis and Computer Vision. We limited experience in these, however we have taken a linear algebra course in college and have good knowledge of python as a programming language. Our motivation for taking up the scikit project is to learn image analysis and computer vision. > > We had already mailed Mr Nunez-Iglesias, and receives a very prompt and helpful reply. After talking with our coach, we came to realise that the issues for us to solve wouldn't require much of either. We were wondering in case we chose this project would we be able to further our knowledge in the areas of image analysis and computer vision and work on issues in this domain? > > Hoping for a quick reply, > > Thanks and Regards > -- > > Y S Ramya > Member, Placement Committee > Coordinator, Rang > Directi Campus Ambassador > Member Media-Panel(Content) > CSE undergrad, IIIT Delhi > +91 8375895350 > > > > > > _______________________________________________ > scikit-image mailing list > scikit-image(a)python.org > https://mail.python.org/mailman/listinfo/scikit-image

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RGSoC project : scikit-image
by Ramya Y S 13 Feb '17

13 Feb '17

Hey We (my teammate, Akarsha is cc'ed ) are interested in Image Analysis and Computer Vision. We limited experience in these, however we have taken a linear algebra course in college and have good knowledge of python as a programming language. Our motivation for taking up the scikit project is to learn image analysis and computer vision. We had already mailed Mr Nunez-Iglesias, and receives a very prompt and helpful reply. After talking with our coach, we came to realise that the issues for us to solve wouldn't require much of either. We were wondering in case we chose this project would we be able to further our knowledge in the areas of image analysis and computer vision and work on issues in this domain? Hoping for a quick reply, Thanks and Regards -- *Y S Ramya* Member, Placement Committee Coordinator, Rang Directi Campus Ambassador Member Media-Panel(Content) CSE undergrad, IIIT Delhi +91 8375895350

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Re: [scikit-image] Import error of threshold_niblack & threshold_sauvola
by Juan Nunez-Iglesias 13 Feb '17

13 Feb '17

Ah! Well good work on troubleshooting compilation! Typically when this happens the problem is that Python is picking up your "standard" install of scikit image. Are you using Anaconda? If so maybe you should try conda uninstall scikit-image and then, in your skimage source directory: pip install -U [--no-deps] -e . (Including the dot at the end. The no-deps is optional and good when you're sure you already have the dependencies.) This is now the preferred way to make an editable install of a package. Updating the docs to reflect this might make a great first contribution! =) Juan. On 13 Feb 2017, 3:09 PM +1000, Sarwat Fatima <sarwatfatimam(a)gmail.com>, wrote: > Yes, it's an import error. However, I cloned scikit-image and build the source using python setup.py develop. It was successful after installing the right compilers, but I am still receiving the import error. > > On 13/02/2017 3:19 AM, <scikit-image-request(a)python.org (mailto:scikit-image-request@python.org)> wrote: > > Send scikit-image mailing list submissions to > > scikit-image(a)python.org (mailto:scikit-image@python.org) > > > > To subscribe or unsubscribe via the World Wide Web, visit > > https://mail.python.org/mailman/listinfo/scikit-image > > or, via email, send a message with subject or body 'help' to > > scikit-image-request(a)python.org (mailto:scikit-image-request@python.org) > > > > You can reach the person managing the list at > > scikit-image-owner(a)python.org (mailto:scikit-image-owner@python.org) > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of scikit-image digest..." > > > > > > Today's Topics: > > > > 1. Re: Installing scikit-image dev (Stefan van der Walt) > > 2. Re: Installing scikit-image dev (Juan Nunez-Iglesias) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Sun, 12 Feb 2017 12:07:55 -0800 > > From: Stefan van der Walt <stefanv(a)berkeley.edu (mailto:stefanv@berkeley.edu)> > > To: scikit-image(a)python.org (mailto:scikit-image@python.org) > > Subject: Re: [scikit-image] Installing scikit-image dev > > Message-ID: > > <1486930075.84793.878619048.772F0B2B(a)webmail.messagingengine.com (mailto:1486930075.84793.878619048.772F0B2B@webmail.messagingengine.com)> > > Content-Type: text/plain; charset="utf-8" > > > > Hi, > > > > > > > > Can you please post the error you get when trying to import those > > filters? > > > > > > Thanks > > > > St?fan > > > > > > > > > > > > On Sat, Feb 11, 2017, at 14:22, Sarwat Fatima wrote: > > > > > Hello, > > > > > > > > > > I wanted to try out the example code of > > > filters.threshold_{niblack,sauvola}from the dev docs but it gave an > > > import error for both threshold filters. So I cloned scikit-image > > > repository and tried python setup.py develop from the root directory > > > but it resulted in an error i.e. "Unable to find vcvarsall.bat". > > > > > > > > I am using Anaconda 4.0.0 version, Python 3.5, Windows 8.1. > > > > > > > > > > How can I install 0.13 version of scikit-image? > > > > > > > > > > Thankyou. > > > > > _________________________________________________ > > > > > scikit-image mailing list > > > > > scikit-image(a)python.org (mailto:scikit-image@python.org) > > > > > https://mail.python.org/mailman/listinfo/scikit-image > > > > > >

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Re: [scikit-image] Import error of threshold_niblack & threshold_sauvola
by Sarwat Fatima 13 Feb '17

13 Feb '17

Yes, it's an import error. However, I cloned scikit-image and build the source using python setup.py develop. It was successful after installing the right compilers, but I am still receiving the import error. On 13/02/2017 3:19 AM, <scikit-image-request(a)python.org> wrote: Send scikit-image mailing list submissions to scikit-image(a)python.org To subscribe or unsubscribe via the World Wide Web, visit https://mail.python.org/mailman/listinfo/scikit-image or, via email, send a message with subject or body 'help' to scikit-image-request(a)python.org You can reach the person managing the list at scikit-image-owner(a)python.org When replying, please edit your Subject line so it is more specific than "Re: Contents of scikit-image digest..." Today's Topics: 1. Re: Installing scikit-image dev (Stefan van der Walt) 2. Re: Installing scikit-image dev (Juan Nunez-Iglesias) ---------------------------------------------------------------------- Message: 1 Date: Sun, 12 Feb 2017 12:07:55 -0800 From: Stefan van der Walt <stefanv(a)berkeley.edu> To: scikit-image(a)python.org Subject: Re: [scikit-image] Installing scikit-image dev Message-ID: <1486930075.84793.878619048.772F0B2B(a)webmail.messagingengine.com> Content-Type: text/plain; charset="utf-8" Hi, Can you please post the error you get when trying to import those filters? Thanks St?fan On Sat, Feb 11, 2017, at 14:22, Sarwat Fatima wrote: > Hello, > > I wanted to try out the example code of > filters.threshold_{niblack,sauvola}from the dev docs but it gave an > import error for both threshold filters. So I cloned scikit-image > repository and tried python setup.py develop from the root directory > but it resulted in an error i.e. "Unable to find vcvarsall.bat". > > I am using Anaconda 4.0.0 version, Python 3.5, Windows 8.1. > > How can I install 0.13 version of scikit-image? > > Thankyou. > _________________________________________________ > scikit-image mailing list > scikit-image(a)python.org > https://mail.python.org/mailman/listinfo/scikit-image

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Re: [scikit-image] Installing scikit-image dev
by Stefan van der Walt 13 Feb '17

13 Feb '17

Hi, Can you please post the error you get when trying to import those filters? Thanks Stéfan On Sat, Feb 11, 2017, at 14:22, Sarwat Fatima wrote: > Hello, > > I wanted to try out the example code of > filters.threshold_{niblack,sauvola}from the dev docs but it gave an > import error for both threshold filters. So I cloned scikit-image > repository and tried python setup.py develop from the root directory > but it resulted in an error i.e. "Unable to find vcvarsall.bat". > > I am using Anaconda 4.0.0 version, Python 3.5, Windows 8.1. > > How can I install 0.13 version of scikit-image? > > Thankyou. > _________________________________________________ > scikit-image mailing list > scikit-image(a)python.org > https://mail.python.org/mailman/listinfo/scikit-image

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