From sarwatfatimam at gmail.com Fri Feb 3 12:57:42 2017 From: sarwatfatimam at gmail.com (Sarwat Fatima) Date: Fri, 3 Feb 2017 22:57:42 +0500 Subject: [scikit-image] Remote Coaches for RGSoC 2017 Message-ID: Hello, I am interested in applying for Scikit-image project in Rails Girls Summer of Code 2017 and looking for coaches who can guide us through. My background is in neuroinformatics where I have used signal processing & machine learning techniques to process, extract features and classify brain signals (like EEG, MEG). The main tools that I have command on are Matlab and Python. In Python, I have mainly worked with scikit-learn and numpy libraries. I have also worked with MNE and pyriemannian tools for Python. I am currently in talk with two potential team members. I am hoping one of them will be able to give full time for this project. Both have a background in Python development. Since you have already been working with scikit-image, we can get better guidance from you. Kindly let me know if you are interested in coaching us. I am looking forward to your reply. Thank you. Regards, Sarwat Fatima & Aqsa Ahmed. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Sun Feb 5 17:49:07 2017 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Mon, 6 Feb 2017 09:49:07 +1100 Subject: [scikit-image] Remote Coaches for RGSoC 2017 In-Reply-To: References: Message-ID: <2a91c5d3-c8e6-4123-9c67-ef9e54395c21@Spark> Just for the record, we have replied to Sarwat privately to say that we would be glad to coach her team. At least three mentors (myself, Steve Sylvester, and St?fan van der Walt) will be participating this year, so we would definitely encourage more RGSoC applicants! As with GSoC, we encourage candidates to get a pull request accepted to the project before Mar 1. We have a list of "easy to contribute" issues: https://github.com/scikit-image/scikit-image/issues?q=is%3Aissue+is%3Aopen+label%3A%22difficulty%3A+novice%22 Juan. On 4 Feb 2017, 4:58 AM +1100, Sarwat Fatima , wrote: > Hello, > > I am interested in applying for?Scikit-image?project?in Rails Girls Summer of Code 2017 and looking for coaches who can guide us through. My background is in neuroinformatics where I have used signal processing & machine learning techniques to process, extract features and classify brain signals (like EEG, MEG). The main tools that I have command on are Matlab and Python. In Python, I have mainly worked with scikit-learn and numpy?libraries. I have also worked with MNE and pyriemannian?tools for Python. > > I am currently in talk with two potential team members. I am hoping one of them will be able to give full time for this project. Both have a?background in Python development. > > Since you have already been working with?scikit-image, we can get better guidance from you. Kindly let me know if you are interested in coaching us. > > I am looking forward to your reply. Thank you. > > Regards, > Sarwat Fatima & Aqsa Ahmed. > _______________________________________________ > scikit-image mailing list > scikit-image at python.org > https://mail.python.org/mailman/listinfo/scikit-image -------------- next part -------------- An HTML attachment was scrubbed... URL: From winecoding at gmail.com Mon Feb 6 14:02:05 2017 From: winecoding at gmail.com (wine lover) Date: Mon, 6 Feb 2017 13:02:05 -0600 Subject: [scikit-image] crop the image with an angle in skimage Message-ID: Dear All, I am trying to leverage the data augmentation techniques for the image segmentation task. In this blog post (http://benanne.github.io/2014/04/05/galaxy-zoo.html), author discusses the following data augmentation procedure. I am not sure how to perform the crop operation with an angle (the cropped one marked with blue) in skimage? In specific, I do not want the cropped one go beyond the scope of original image. Thanks, [image: Inline image 1] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 235339 bytes Desc: not available URL: From stefanv at berkeley.edu Mon Feb 6 14:23:24 2017 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Mon, 06 Feb 2017 11:23:24 -0800 Subject: [scikit-image] crop the image with an angle in skimage In-Reply-To: References: Message-ID: <1486409004.3466347.872187984.7D3D8812@webmail.messagingengine.com> Hi there, On Mon, Feb 6, 2017, at 11:02, wine lover wrote: > I am not sure how to perform the crop operation with an angle (the > cropped one marked with blue) in skimage? In specific, I do not want > the cropped one go beyond the scope of original image. How about rotating the image, and then doing a square crop? Alternatively, you can do it all in one step with an image transformation. Something like this (untested, read it as pseudocode): in_coords = np.array(...) # coordinates of rotated square out_coords = np.array(...) # coordinates of output image tf = skimage.transform.estimate_transform('euclidian', in_coords, out_coords) cropped_image = skimage.transform.warp(image, tf.inverse) Best regards St?fan -------------- next part -------------- An HTML attachment was scrubbed... URL: From winecoding at gmail.com Mon Feb 6 14:50:32 2017 From: winecoding at gmail.com (wine lover) Date: Mon, 6 Feb 2017 13:50:32 -0600 Subject: [scikit-image] crop the image with an angle in skimage In-Reply-To: References: Message-ID: Hi John, Thanks a lot for your suggestions. There might be a potential issue, for instance, I tried elas_img = transform.rotate(image=img,angle=45) The original image and rotated image are shown as follows. It can be seen that the rotated image gets four corner areas cut. I am not sure whether I will lose any content from there. For example, I can get a sample patch from the left bottom corner of the original image; but this left bottom corner was cut in the rotated image. [image: Inline image 1] On Mon, Feb 6, 2017 at 1:07 PM, John Jenkinson wrote: > rotate the image by 45 degrees then crop the red square and you will have > the blue square > > On Feb 6, 2017 1:02 PM, "wine lover" wrote: > > Dear All, > > I am trying to leverage the data augmentation techniques for the image > segmentation task. > > In this blog post (http://benanne.github.io/2014/04/05/galaxy-zoo.html > ), author discusses the following data augmentation procedure. > > I am not sure how to perform the crop operation with an angle (the cropped > one marked with blue) in skimage? In specific, I do not want the cropped > one go beyond the scope of original image. > > Thanks, > > > [image: Inline image 1] > > _______________________________________________ > scikit-image mailing list > scikit-image at python.org > https://mail.python.org/mailman/listinfo/scikit-image > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 235339 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 173911 bytes Desc: not available URL: From sarwatfatimam at gmail.com Sat Feb 11 17:22:38 2017 From: sarwatfatimam at gmail.com (Sarwat Fatima) Date: Sun, 12 Feb 2017 03:22:38 +0500 Subject: [scikit-image] Installing scikit-image dev Message-ID: 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Sun Feb 12 15:07:55 2017 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Sun, 12 Feb 2017 12:07:55 -0800 Subject: [scikit-image] Installing scikit-image dev In-Reply-To: References: Message-ID: <1486930075.84793.878619048.772F0B2B@webmail.messagingengine.com> 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 at python.org > https://mail.python.org/mailman/listinfo/scikit-image -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Sun Feb 12 17:17:44 2017 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Mon, 13 Feb 2017 08:17:44 +1000 Subject: [scikit-image] Installing scikit-image dev In-Reply-To: <1486930075.84793.878619048.772F0B2B@webmail.messagingengine.com> References: <1486930075.84793.878619048.772F0B2B@webmail.messagingengine.com> Message-ID: <109338f2-2756-42a1-a46d-8a84d6975ebc@Spark> I'm pretty sure it'll be an import error since those aren't in 0.12... On 13 Feb 2017, 6:08 AM +1000, Stefan van der Walt , wrote: > 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 at python.org (mailto:scikit-image at python.org) > > https://mail.python.org/mailman/listinfo/scikit-image > > _______________________________________________ > scikit-image mailing list > scikit-image at python.org > https://mail.python.org/mailman/listinfo/scikit-image -------------- next part -------------- An HTML attachment was scrubbed... URL: From sarwatfatimam at gmail.com Mon Feb 13 00:08:42 2017 From: sarwatfatimam at gmail.com (Sarwat Fatima) Date: Mon, 13 Feb 2017 10:08:42 +0500 Subject: [scikit-image] Import error of threshold_niblack & threshold_sauvola In-Reply-To: References: Message-ID: 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, wrote: Send scikit-image mailing list submissions to scikit-image at 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 at python.org You can reach the person managing the list at scikit-image-owner at 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 To: scikit-image at python.org Subject: Re: [scikit-image] Installing scikit-image dev Message-ID: <1486930075.84793.878619048.772F0B2B at 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 at python.org > https://mail.python.org/mailman/listinfo/scikit-image -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 2 Date: Mon, 13 Feb 2017 08:17:44 +1000 From: Juan Nunez-Iglesias To: scikit-image at python.org, Stefan van der Walt Subject: Re: [scikit-image] Installing scikit-image dev Message-ID: <109338f2-2756-42a1-a46d-8a84d6975ebc at Spark> Content-Type: text/plain; charset="utf-8" I'm pretty sure it'll be an import error since those aren't in 0.12... On 13 Feb 2017, 6:08 AM +1000, Stefan van der Walt , wrote: > 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 at python.org (mailto:scikit-image at python.org) > > https://mail.python.org/mailman/listinfo/scikit-image > > _______________________________________________ > scikit-image mailing list > scikit-image at python.org > https://mail.python.org/mailman/listinfo/scikit-image -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ scikit-image mailing list scikit-image at python.org https://mail.python.org/mailman/listinfo/scikit-image ------------------------------ End of scikit-image Digest, Vol 5, Issue 6 ****************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Mon Feb 13 00:44:15 2017 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Mon, 13 Feb 2017 15:44:15 +1000 Subject: [scikit-image] Import error of threshold_niblack & threshold_sauvola In-Reply-To: References: Message-ID: <3d233f2b-bb49-44a5-af2c-b0c773b57118@Spark> 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 , 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, wrote: > > Send scikit-image mailing list submissions to > > scikit-image at python.org (mailto:scikit-image at 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 at python.org (mailto:scikit-image-request at python.org) > > > > You can reach the person managing the list at > > scikit-image-owner at python.org (mailto:scikit-image-owner at 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 > > To: scikit-image at python.org (mailto:scikit-image at python.org) > > Subject: Re: [scikit-image] Installing scikit-image dev > > Message-ID: > > <1486930075.84793.878619048.772F0B2B at webmail.messagingengine.com (mailto:1486930075.84793.878619048.772F0B2B at 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 at python.org (mailto:scikit-image at python.org) > > > > > https://mail.python.org/mailman/listinfo/scikit-image > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Message: 2 > > Date: Mon, 13 Feb 2017 08:17:44 +1000 > > From: Juan Nunez-Iglesias > > To: scikit-image at python.org (mailto:scikit-image at python.org), Stefan van der Walt > > > > Subject: Re: [scikit-image] Installing scikit-image dev > > Message-ID: <109338f2-2756-42a1-a46d-8a84d6975ebc at Spark> > > Content-Type: text/plain; charset="utf-8" > > > > I'm pretty sure it'll be an import error since those aren't in 0.12... > > > > On 13 Feb 2017, 6:08 AM +1000, Stefan van der Walt , wrote: > > > 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 at python.org (mailto:scikit-image at python.org) (mailto:scikit-image at python.org) > > > > https://mail.python.org/mailman/listinfo/scikit-image > > > > > > _______________________________________________ > > > scikit-image mailing list > > > scikit-image at python.org (mailto:scikit-image at python.org) > > > https://mail.python.org/mailman/listinfo/scikit-image > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > > ------------------------------ > > > > Subject: Digest Footer > > > > _______________________________________________ > > scikit-image mailing list > > scikit-image at python.org (mailto:scikit-image at python.org) > > https://mail.python.org/mailman/listinfo/scikit-image > > > > > > ------------------------------ > > > > End of scikit-image Digest, Vol 5, Issue 6 > > ****************************************** > > _______________________________________________ > scikit-image mailing list > scikit-image at python.org > https://mail.python.org/mailman/listinfo/scikit-image -------------- next part -------------- An HTML attachment was scrubbed... URL: From yellapragada15117 at iiitd.ac.in Mon Feb 13 09:58:59 2017 From: yellapragada15117 at iiitd.ac.in (Ramya Y S) Date: Mon, 13 Feb 2017 20:28:59 +0530 Subject: [scikit-image] RGSoC project : scikit-image Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From steven.silvester at gmail.com Mon Feb 13 14:24:52 2017 From: steven.silvester at gmail.com (Steven Silvester) Date: Mon, 13 Feb 2017 13:24:52 -0600 Subject: [scikit-image] RGSoC project : scikit-image In-Reply-To: References: Message-ID: 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 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 at python.org > https://mail.python.org/mailman/listinfo/scikit-image -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Mon Feb 13 14:26:16 2017 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Mon, 13 Feb 2017 11:26:16 -0800 Subject: [scikit-image] Do we trust image measurements? Message-ID: <1487013976.3323611.879725624.3857A0C4@webmail.messagingengine.com> 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). St?fan [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." From soumyag213 at gmail.com Wed Feb 15 13:58:49 2017 From: soumyag213 at gmail.com (Soumya Gupta) Date: Thu, 16 Feb 2017 00:28:49 +0530 Subject: [scikit-image] Introductory shoutout Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From steven.silvester at gmail.com Thu Feb 16 04:55:46 2017 From: steven.silvester at gmail.com (Steven Silvester) Date: Thu, 16 Feb 2017 03:55:46 -0600 Subject: [scikit-image] Introductory shoutout In-Reply-To: References: Message-ID: <6D4C2B18-3613-4D19-990C-076BF0737115@gmail.com> Hello Soumya and Vibhuti, and welcome! Regards, Steve > On Feb 15, 2017, at 12:58 PM, Soumya Gupta 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 at python.org > https://mail.python.org/mailman/listinfo/scikit-image From stefanv at berkeley.edu Thu Feb 16 17:27:44 2017 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Thu, 16 Feb 2017 14:27:44 -0800 Subject: [scikit-image] Announcing: Docathon, week of 6 March 2017 Message-ID: <1487284064.3300438.883629080.6FBC0B05@webmail.messagingengine.com> 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 St?fan *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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Thu Feb 16 18:07:01 2017 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Thu, 16 Feb 2017 15:07:01 -0800 Subject: [scikit-image] Squash merges Message-ID: <1487286421.3309409.883666288.5D554294@webmail.messagingengine.com> 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 St?fan From sanyabt11 at gmail.com Sat Feb 18 05:19:42 2017 From: sanyabt11 at gmail.com (Sanya B. Taneja) Date: Sat, 18 Feb 2017 15:49:42 +0530 Subject: [scikit-image] scikit-image RGSoC 2017 Message-ID: Hi, My teammate (Anshita Gupta) and I are interested in applying for the project ?scikit-image? for RGSoC 2017. We have a background in Computer Science and programming in Python, as well as some experience working with numpy and scikit-learn packages on Jupyter Notebook. In the past few weeks we have- - Read the user guide and guidelines for contribution on scikit-image.org . - Implemented the online tutorials and examples using Jupyter Notebook. - Begun to solve novice issues on GitHub and had one PR merged with the master. Another is in progress. Our insight into this package and attempts to solve the novice issues have been very interesting and compelling and we would love to further delve into the project by solving the challenges, working on medium and hard issues and contributing to the code! Looking forward to working further, Regards Sanya B. Taneja CSE Undergraduate (2014-18) -------------- next part -------------- An HTML attachment was scrubbed... URL: From steven.silvester at gmail.com Sat Feb 18 13:43:40 2017 From: steven.silvester at gmail.com (Steven Silvester) Date: Sat, 18 Feb 2017 18:43:40 +0000 (UTC) Subject: [scikit-image] scikit-image RGSoC 2017 In-Reply-To: References: Message-ID: Well done Sanya and Anshita! ? ?We are thankful for your contributions and interest.? Regards, Steve _____________________________ From: Sanya B. Taneja Sent: Saturday, February 18, 2017 4:19 AM Subject: [scikit-image] scikit-image RGSoC 2017 To: Cc: Anshita Gupta Hi, My teammate (Anshita Gupta) and I are interested in applying for the project ?scikit-image? for RGSoC 2017. We have a background in Computer Science and programming in Python, as well as some experience working with numpy and scikit-learn packages on Jupyter Notebook.? In the past few weeks we have-Read the user guide and guidelines for contribution on scikit-image.org.Implemented the online tutorials and examples using Jupyter Notebook.?Begun to solve novice issues on GitHub and had one PR merged with the master. Another is in progress.Our insight into this package and attempts to solve the novice issues have been very interesting and compelling and we would love to further delve into the project by solving the challenges, working on medium and hard issues and contributing to the code! Looking forward to working further, RegardsSanya B. TanejaCSE Undergraduate (2014-18) -------------- next part -------------- An HTML attachment was scrubbed... URL: From jillc at enthought.com Mon Feb 20 21:26:47 2017 From: jillc at enthought.com (Jill Cowan) Date: Mon, 20 Feb 2017 20:26:47 -0600 Subject: [scikit-image] SciPy 2017 Message-ID: Hi, Mark Your Calendar for SciPy 2017! July 10-16, 2017 | Austin, Texas SciPy 2017 Tutorials: July 10-11, 2017 SciPy 2017 Conference: July 12-14, 2017 SciPy 2017 Sprints: July 15-16, 2017 Call for Propsals Is Now Open: Submit your talk, poster and tutorial ideas: http://scipy2017.scipy.org/ehome/220975/493425/ The deadline for proposals is March 27th for talks and posters ; March 22nd for tutorials. Financial aid is accepting applications through April 21st http://scipy2017.scipy.org/ehome/220975/493436/ Registration will open February 27th. Learn more about the conference at scipy2017.scipy.org Hope to see you there! -- Jill Cowan Enthought, Inc. jillc at enthought.com 512.536.1057 -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Wed Feb 22 02:38:10 2017 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Tue, 21 Feb 2017 23:38:10 -0800 Subject: [scikit-image] IO documentation In-Reply-To: References: Message-ID: <1487749090.3265070.888913400.50414842@webmail.messagingengine.com> Hi Michael On Thu, Jan 5, 2017, at 01:45, Michal Romaniuk wrote: > The IO documentation doesn't seem to be very good. It explains how > plugins work but it's scarce on examples e.g. on how to export jpeg > image with a specified compression level. The IO API docs don't give > much detail either. Some details can be found in the docs for > external.tifffile but it takes some searching to find it. For PIL the > only way to figure out how to use it seems to be looking at the source > code - no modern docs as far as I can tell (did I fail to use Google > properly?). Thanks for your comment; unfortunately io.imsave does not currently support specifying compression level (that is only supported for TIFF files). That said, you can accomplish this yourself using PIL: In [1]: from skimage.io._plugins.pil_plugin import ndarray_to_pil In [2]: from skimage import data In [3]: img = data.chelsea() In [4]: pil_img = ndarray_to_pil(img) In [5]: pil_img.save('/tmp/chelsea0.jpg', quality=10) In [6]: pil_img.save('/tmp/chelsea1.jpg', quality=90) In [7]: !du -hcs /tmp/chelsea*.jpg 8.0K /tmp/chelsea0.jpg 36K /tmp/chelsea1.jpg Best regards St?fan -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Wed Feb 22 02:38:30 2017 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Tue, 21 Feb 2017 23:38:30 -0800 Subject: [scikit-image] IO documentation In-Reply-To: <1487749090.3265070.888913400.50414842@webmail.messagingengine.com> References: <1487749090.3265070.888913400.50414842@webmail.messagingengine.com> Message-ID: <1487749110.3265070.888915472.533E4339@webmail.messagingengine.com> On Tue, Feb 21, 2017, at 23:38, Stefan van der Walt wrote: > Hi Michael Apologies, Michal. > On Thu, Jan 5, 2017, at 01:45, Michal Romaniuk wrote: >> The IO documentation doesn't seem to be very good. It explains how >> plugins work but it's scarce on examples e.g. on how to export jpeg >> image with a specified compression level. The IO API docs don't give >> much detail either. Some details can be found in the docs for >> external.tifffile but it takes some searching to find it. For PIL the >> only way to figure out how to use it seems to be looking at the >> source code - no modern docs as far as I can tell (did I fail to use >> Google properly?). > > Thanks for your comment; unfortunately io.imsave does not currently > support specifying compression level (that is only supported for > TIFF files). > > That said, you can accomplish this yourself using PIL: > > In [1]: from skimage.io._plugins.pil_plugin import ndarray_to_pil > In [2]: from skimage import data > In [3]: img = data.chelsea() > In [4]: pil_img = ndarray_to_pil(img) > In [5]: pil_img.save('/tmp/chelsea0.jpg', quality=10) > In [6]: pil_img.save('/tmp/chelsea1.jpg', quality=90) > > In [7]: !du -hcs /tmp/chelsea*.jpg > 8.0K /tmp/chelsea0.jpg > 36K /tmp/chelsea1.jpg > > Best regards > St?fan > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Wed Feb 22 02:57:19 2017 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Tue, 21 Feb 2017 23:57:19 -0800 Subject: [scikit-image] Last 3 issues before 0.13 Message-ID: <1487750239.3270000.888927792.09EF2BD5@webmail.messagingengine.com> Hi, everyone If you have a bit of spare time, please help us solve *the last three issues* blocking release of 0.13: https://github.com/scikit-image/scikit-image/issues?q=is%3Aopen+is%3Aissue+milestone%3A0.13 Thank you to everyone who has been working so hard on making this happen. Best regards St?fan From fboulogne at sciunto.org Wed Feb 22 11:04:00 2017 From: fboulogne at sciunto.org (=?UTF-8?Q?Fran=c3=a7ois_Boulogne?=) Date: Wed, 22 Feb 2017 17:04:00 +0100 Subject: [scikit-image] IO documentation In-Reply-To: <1487749090.3265070.888913400.50414842@webmail.messagingengine.com> References: <1487749090.3265070.888913400.50414842@webmail.messagingengine.com> Message-ID: A pull request that proposes the enhance the situation about that: https://github.com/scikit-image/scikit-image/pull/2063 Best, -- Fran?ois Boulogne. http://www.sciunto.org GPG: 32D5F22F From winecoding at gmail.com Wed Feb 22 14:04:46 2017 From: winecoding at gmail.com (wine lover) Date: Wed, 22 Feb 2017 13:04:46 -0600 Subject: [scikit-image] the mechanism and implementation of generating a subimage from a large image Message-ID: Hi All, I have a set of image pairs, i.e., {A, A?}, {B, B?}, {C,C?} etc. Given an image A, for instance, 256*256, are there any sampling mechanisms to generate a small image, i.e., 128*128, that can capture the global contexts of original images. At the same time, I would like to keep track information of those sampled pixels. For instance, if pixel[I,J] in A is selected, I need to track it because I need to select the same pixel of A?. In other words, I need to generate a set of smaller image pairs based on these large image pairs. The sampling mechanism, however, is based on A, B, C, etc; and A?, B?,C? are just sampled accordingly. Are there any skimage functions that I can use? Thanks, -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Wed Feb 22 15:20:21 2017 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Wed, 22 Feb 2017 12:20:21 -0800 Subject: [scikit-image] the mechanism and implementation of generating a subimage from a large image In-Reply-To: References: Message-ID: <1487794821.166404.889681600.2A00B7BE@webmail.messagingengine.com> Hi wl, It is unclear whether you want to extract features from each image, or whether you want to downsample the images to represent the originals. If you want to downsample, I'd recommend http://scikit-image.org/docs/dev/api/skimage.transform.html#skimage.transform.downscale_local_mean otherwise, use e.g., histogram of gradients as features. Best regards St?fan On Wed, Feb 22, 2017, at 11:04, wine lover wrote: > Hi All, > > I have a set of image pairs, i.e., {A, A?}, {B, B?}, {C,C?} etc. > > Given an image A, for instance, 256*256, are there any sampling > mechanisms to generate a small image, i.e., 128*128, that can capture > the global contexts of original images. At the same time, I would > like to keep track information of those sampled pixels. For instance, > if pixel[I,J] in A is selected, I need to track it because I need to > select the same pixel of A?. > > In other words, I need to generate a set of smaller image pairs based > on these large image pairs. The sampling mechanism, however, is based > on A, B, C, etc; and A?, B?,C? are just sampled accordingly. > > Are there any skimage functions that I can use? > > Thanks, > > _________________________________________________ > scikit-image mailing list > scikit-image at python.org > https://mail.python.org/mailman/listinfo/scikit-image -------------- next part -------------- An HTML attachment was scrubbed... URL: From sanyabt11 at gmail.com Fri Feb 24 04:41:42 2017 From: sanyabt11 at gmail.com (Sanya B. Taneja) Date: Fri, 24 Feb 2017 15:11:42 +0530 Subject: [scikit-image] RGSoC'17 Coaches (Remote) In-Reply-To: References: Message-ID: Hi, We've almost completed our application for RGSoC'17 and are psyched to have a chance to explore this project. We read the description on the RGSoC website stating that 3 members of the core contributor team have signed up to coach the teams. We would love to have some of the scikit-image contributors as our coaches (remote). Kindly get back to us if you'll be interested in the same. Hoping for a quick response. Thanks Sanya B. Taneja (Team Allonsy) -------------- next part -------------- An HTML attachment was scrubbed... URL: