From siqueiraaf at gmail.com Thu Sep 1 08:21:35 2016 From: siqueiraaf at gmail.com (Alexandre Fioravante de Siqueira) Date: Thu, 1 Sep 2016 05:21:35 -0700 (PDT) Subject: Fwd: PyData Community Cookbook - August Update In-Reply-To: <1472680444.2684150.712061369.2AC87F0C@webmail.messagingengine.com> References: <1472501613.509939.709586801.1704EAF6@webmail.messagingengine.com> <20160829204435.GC1302378@phare.normalesup.org> <1472576802.757608.710583985.061974DE@webmail.messagingengine.com> <20160830192254.GA1722536@phare.normalesup.org> <1472680444.2684150.712061369.2AC87F0C@webmail.messagingengine.com> Message-ID: Hi all, St?fan, thanks for that. I'm working on it. I need your e-mails and institutions for the commit: """ :author: St?fan van der Walt :email: :institution: :corresponding: :author: Emmanuelle Gouillart :email: :institution: :institution: :equal-contributor: :author: Egor Panfilov :email: :institution: :equal-contributor: :author: Alexandre de Siqueira :email: :institution: University of Campinas :institution: TU Bergakademie Freiberg :equal-contributor: """ We need an abstract too: """ scikit-image is an image processing toolbox for SciPy which provides easy access for segmentation, geometric transformations, color space manipulation, analysis, filtering, morphology, feature detection, and more. It is available free of charge and restriction, and the code is written by an active community of volunteers. (...) """ As you may see I need some ideas for that :) Since this is a cookbook, I think it would be aimed to "recipes" using different functions/objects from the library. Maybe we could specify some examples on the abstract. Do you have any ideas? I'll wait until 10hPM (Berlin time; 8hPM UTC) to submit that, so we can discuss some ideas if you have time. Thanks! I'm here if you need. Kind regards, Alex Em quarta-feira, 31 de agosto de 2016 23:54:06 UTC+2, stefanv escreveu: > > Hi Alex > > On Wed, Aug 31, 2016, at 10:41, Alexandre Fioravante de Siqueira wrote: > > have you figured it out? The deadline is tomorrow, and I would really > > like to participate. > > Would you please submit an initial pull request on the team's behalf? > You can add me, Egor, Emmanuelle, and anyone else who expresses interest > here as co-authors. > > Emmanuelle, I will double check that the chapter is fully open when it > is done so that we can remix parts for the user guide. > > Thanks > St?fan > -------------- next part -------------- An HTML attachment was scrubbed... URL: From emmanuelle.gouillart at nsup.org Thu Sep 1 03:29:03 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Thu, 1 Sep 2016 09:29:03 +0200 Subject: Distance Estimation In-Reply-To: References: <1472685144.113590.712117217.1B48040B@webmail.messagingengine.com> Message-ID: <20160901072903.GA2668326@phare.normalesup.org> Hi Chris, the short version is no, there is no function in scikit-image that can do what the Stanford paper does. However, you can find some useful building blocks in scikit-image and scikit-learn, that you can put together to build your own version of the algorithm (from what I figured out after a quick reading of http://www.cs.cornell.edu/~asaxena/reconstruction3d/saxena_iccv_3drr07_learning3d.pdf) - Felzenswalb superpixels are available in skimage.segmentation (http://scikit-image.org/docs/dev/auto_examples/segmentation/plot_segmentations.html) - Local features can be computed using several functions of scikit-image, such as color transforms (color.ycbcr) and edge filters (filters.sobel_h, filters.sobel_v, ...) - A logistic regression algorithm is available in scikit-learn (http://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html) The trickiest part to code would be the MAP inference on the MRF, where I guess you would have to code it yourself (I think). So, it is feasible to assemble these different blocks, but it's not a small project either. As for other libraries, I'm afraid nothing comes to my mind. OpenCV does have a depth estimation function, but only from stereo images. Hope this helps, Emma On Wed, Aug 31, 2016 at 09:30:20PM -0400, Chris Spencer wrote: > Essentially, what's described here: > http://www.cs.cornell.edu/~asaxena/learningdepth/ > On Wed, Aug 31, 2016 at 9:29 PM, Chris Spencer wrote: > Given a JPG image of a scene, convert that into a depth map, where each > pixel is associated with a discrete distance estimate. > On Wed, Aug 31, 2016 at 7:12 PM, Stefan van der Walt > wrote: > Hi Chris > On Sun, Aug 28, 2016, at 17:31, Chris Spencer wrote: > > Is there any algorithm in scikit-image that I could use to train a > predictor that could estimate the distance at each pixel in an image? > > I've gone through all the examples, and none of them seemed to > directly apply. The image segmentation example seemed to be the > closest, but that didn't use supervised learning, so I wasn't sure how > I could adapt it's code. > Could you explain what you mean by "estimate the distance"? > St??fan From chrisspen at gmail.com Thu Sep 1 11:41:24 2016 From: chrisspen at gmail.com (Chris Spencer) Date: Thu, 1 Sep 2016 11:41:24 -0400 Subject: Distance Estimation In-Reply-To: <20160901072903.GA2668326@phare.normalesup.org> References: <1472685144.113590.712117217.1B48040B@webmail.messagingengine.com> <20160901072903.GA2668326@phare.normalesup.org> Message-ID: Thanks, that's what I was looking for. On Thu, Sep 1, 2016 at 3:29 AM, Emmanuelle Gouillart < emmanuelle.gouillart at nsup.org> wrote: > Hi Chris, > > the short version is no, there is no function in scikit-image that can do > what the Stanford paper does. However, you can find some useful building > blocks in scikit-image and scikit-learn, that you can put together to > build your own version of the algorithm (from what I figured out after > a quick reading of > http://www.cs.cornell.edu/~asaxena/reconstruction3d/ > saxena_iccv_3drr07_learning3d.pdf) > > - Felzenswalb superpixels are available in skimage.segmentation > (http://scikit-image.org/docs/dev/auto_examples/segmentation/plot_ > segmentations.html) > - Local features can be computed using several functions of scikit-image, > such as color transforms (color.ycbcr) and edge filters > (filters.sobel_h, filters.sobel_v, ...) > - A logistic regression algorithm is available in scikit-learn > (http://scikit-learn.org/stable/modules/generated/sklearn.linear_model. > LogisticRegression.html) > > The trickiest part to code would be the MAP inference on the MRF, where I > guess you would have to code it yourself (I think). > > So, it is feasible to assemble these different blocks, but it's not a > small project either. > > As for other libraries, I'm afraid nothing comes to my mind. OpenCV does > have a depth estimation function, but only from stereo images. > > Hope this helps, > Emma > > > On Wed, Aug 31, 2016 at 09:30:20PM -0400, Chris Spencer wrote: > > Essentially, what's described here: > > > http://www.cs.cornell.edu/~asaxena/learningdepth/ > > > On Wed, Aug 31, 2016 at 9:29 PM, Chris Spencer > wrote: > > > Given a JPG image of a scene, convert that into a depth map, where > each > > pixel is associated with a discrete distance estimate. > > > On Wed, Aug 31, 2016 at 7:12 PM, Stefan van der Walt < > stefanv at berkeley.edu> > > wrote: > > > Hi Chris > > > On Sun, Aug 28, 2016, at 17:31, Chris Spencer wrote: > > > Is there any algorithm in scikit-image that I could use to > train a > > predictor that could estimate the distance at each pixel in an > image? > > > > I've gone through all the examples, and none of them seemed to > > directly apply. The image segmentation example seemed to be the > > closest, but that didn't use supervised learning, so I wasn't > sure how > > I could adapt it's code. > > > Could you explain what you mean by "estimate the distance"? > > > St?fan > > -- > 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/qvGm0zOv2rc/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > scikit-image+unsubscribe at googlegroups.com. > To post to this group, send an email to scikit-image at googlegroups.com. > To view this discussion on the web, visit https://groups.google.com/d/ > msgid/scikit-image/20160901072903.GA2668326%40phare.normalesup.org. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From siqueiraaf at gmail.com Thu Sep 1 16:14:08 2016 From: siqueiraaf at gmail.com (Alexandre Fioravante de Siqueira) Date: Thu, 1 Sep 2016 13:14:08 -0700 (PDT) Subject: Fwd: PyData Community Cookbook - August Update In-Reply-To: <20160901170037.GB3064887@phare.normalesup.org> References: <1472501613.509939.709586801.1704EAF6@webmail.messagingengine.com> <20160829204435.GC1302378@phare.normalesup.org> <1472576802.757608.710583985.061974DE@webmail.messagingengine.com> <20160830192254.GA1722536@phare.normalesup.org> <1472680444.2684150.712061369.2AC87F0C@webmail.messagingengine.com> <20160901170037.GB3064887@phare.normalesup.org> Message-ID: <8056474b-c088-4f75-9c5f-441f62c53c74@googlegroups.com> Hi all, we're in! I think... I sent the pull request: http://github.com/pydata/pydata-cookbook/pull/6 * Egor: sorry man, I didn't find any info about you. However, I added your name. I'll wait for the other information, ok? * St?fan: I got your info on BIDS site. Please check if there's something I need to change. * Emma: thank you very much for sending your data, I had only your previous e-mail. I used the abstract you sent, thanks for helping with that. I think you're right about the "cookbook" think, we have space for doing an overview of scikit-image and presenting some nice stuff :) """ How about we select one example if each of the chapters of the gallery and we take advantage of the cookbook to improve it? """ That would be great! Now I'm waiting for the action. Kind regards y'all, have a nice night. Alex Em quinta-feira, 1 de setembro de 2016 19:00:40 UTC+2, Emmanuelle Gouillart escreveu: > > > Hi Alexandre, > > thanks for taking care of this. > > My details > e-mail: emmanuelle... at nsup.org > institution: Joint Unit CNRS/Saint-Gobain Surface of Glass and > Interfaces, Aubervilliers, France > > For the abstract I think you can also re-use materials from the > scikit-image paper, the abstract is > > ******** > scikit-image is an image processing library that implements algorithms > and utilities for use in research, education and industry applications. > It is released under the liberal Modified BSD open source license, > provides a well-documented API in the Python programming language, and is > developed by an active, international team of collaborators. In this > paper we highlight the advantages of open source to achieve the goals of > the scikit-image library, and we showcase several real-world image > processing applications that use scikit-image. More information can be > found on the project homepage, http://scikit-image.org. > ******** > > Don't worry too much about the abstract now, we'll have time to change > it. I'm not sure we have to give examples in the abstract, which should > be general enough. > > But it's a good time to start thinking about the content. Even if it's > advertised as a "cookbook", I think that a length of 15-20 pages is > enough to present both "recipes" and also some big picture stuff (why and > when use scikit-image or other image processing libraries? what are the > typical coding patterns? etc.). As for the recipes, if we can re-use some > of our gallery examples it will save us some precious time. How about we > select one example if each of the chapters of the gallery and we take > advantage of the cookbook to improve it? > > Best, > Emma > > On Thu, Sep 01, 2016 at 05:21:35AM -0700, Alexandre Fioravante de Siqueira > wrote: > > Hi all, > > St?fan, thanks for that. I'm working on it. > > I need your e-mails and institutions for the commit: > > > """ > > :author: St?fan van der Walt > > :email: > > :institution: > > :corresponding: > > > :author: Emmanuelle Gouillart > > :email: > > :institution: > > :institution: > > :equal-contributor: > > > :author: Egor Panfilov > > :email: > > :institution: > > :equal-contributor: > > > :author: Alexandre de Siqueira > > :email: > > :institution: University of Campinas > > :institution: TU Bergakademie Freiberg > > :equal-contributor: > > """ > > > We need an abstract too: > > > """ > > scikit-image is an image processing toolbox for SciPy which provides > easy > > access for segmentation, geometric transformations, color space > manipulation, > > analysis, filtering, morphology, feature detection, and more. It is > available > > free of charge and restriction, and the code is written by an > active community > > of volunteers. > > > (...) > > """ > > > As you may see I need some ideas for that :) Since this is a cookbook, I > think > > it would be aimed to "recipes" using different functions/objects from > the > > library. Maybe we could specify some examples on the abstract. Do you > have any > > ideas? > > I'll wait until 10hPM (Berlin time; 8hPM UTC) to submit that, so we can > discuss > > some ideas if you have time. > > Thanks! I'm here if you need. > > Kind regards, > > > Alex > > > Em quarta-feira, 31 de agosto de 2016 23:54:06 UTC+2, stefanv escreveu: > > > Hi Alex > > > On Wed, Aug 31, 2016, at 10:41, Alexandre Fioravante de Siqueira > wrote: > > > have you figured it out? The deadline is tomorrow, and I would > really > > > like to participate. > > > Would you please submit an initial pull request on the team's > behalf? > > You can add me, Egor, Emmanuelle, and anyone else who expresses > interest > > here as co-authors. > > > Emmanuelle, I will double check that the chapter is fully open when > it > > is done so that we can remix parts for the user guide. > > > Thanks > > St?fan > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Thu Sep 1 20:52:15 2016 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Thu, 01 Sep 2016 17:52:15 -0700 Subject: Fwd: PyData Community Cookbook - August Update In-Reply-To: <8056474b-c088-4f75-9c5f-441f62c53c74@googlegroups.com> References: <1472501613.509939.709586801.1704EAF6@webmail.messagingengine.com> <20160829204435.GC1302378@phare.normalesup.org> <1472576802.757608.710583985.061974DE@webmail.messagingengine.com> <20160830192254.GA1722536@phare.normalesup.org> <1472680444.2684150.712061369.2AC87F0C@webmail.messagingengine.com> <20160901170037.GB3064887@phare.normalesup.org> <8056474b-c088-4f75-9c5f-441f62c53c74@googlegroups.com> Message-ID: <1472777535.1016360.713353281.15440D94@webmail.messagingengine.com> On Thu, Sep 1, 2016, at 13:14, Alexandre Fioravante de Siqueira wrote: > """ > How about we select one example if each of the chapters of the gallery > and we take advantage of the cookbook to improve it? > """ We can also select some material from the scipy lectures we've given in the past. E.g., I think the RANSAC lecture went down well: https://github.com/scikit-image/skimage-tutorials/blob/master/lectures/5_ransac.ipynb St?fan -------------- next part -------------- An HTML attachment was scrubbed... URL: From emmanuelle.gouillart at nsup.org Thu Sep 1 13:00:37 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Thu, 1 Sep 2016 19:00:37 +0200 Subject: Fwd: PyData Community Cookbook - August Update In-Reply-To: References: <1472501613.509939.709586801.1704EAF6@webmail.messagingengine.com> <20160829204435.GC1302378@phare.normalesup.org> <1472576802.757608.710583985.061974DE@webmail.messagingengine.com> <20160830192254.GA1722536@phare.normalesup.org> <1472680444.2684150.712061369.2AC87F0C@webmail.messagingengine.com> Message-ID: <20160901170037.GB3064887@phare.normalesup.org> Hi Alexandre, thanks for taking care of this. My details e-mail: emmanuelle.gouillart at nsup.org institution: Joint Unit CNRS/Saint-Gobain Surface of Glass and Interfaces, Aubervilliers, France For the abstract I think you can also re-use materials from the scikit-image paper, the abstract is ******** scikit-image is an image processing library that implements algorithms and utilities for use in research, education and industry applications. It is released under the liberal Modified BSD open source license, provides a well-documented API in the Python programming language, and is developed by an active, international team of collaborators. In this paper we highlight the advantages of open source to achieve the goals of the scikit-image library, and we showcase several real-world image processing applications that use scikit-image. More information can be found on the project homepage, http://scikit-image.org. ******** Don't worry too much about the abstract now, we'll have time to change it. I'm not sure we have to give examples in the abstract, which should be general enough. But it's a good time to start thinking about the content. Even if it's advertised as a "cookbook", I think that a length of 15-20 pages is enough to present both "recipes" and also some big picture stuff (why and when use scikit-image or other image processing libraries? what are the typical coding patterns? etc.). As for the recipes, if we can re-use some of our gallery examples it will save us some precious time. How about we select one example if each of the chapters of the gallery and we take advantage of the cookbook to improve it? Best, Emma On Thu, Sep 01, 2016 at 05:21:35AM -0700, Alexandre Fioravante de Siqueira wrote: > Hi all, > St??fan, thanks for that. I'm working on it. > I need??your e-mails and institutions??for the commit: > """ > :author: St??fan van der Walt > :email:?? > :institution:?? > :corresponding: > :author: Emmanuelle Gouillart > :email:?? > :institution:?? > :institution:?? > :equal-contributor: > :author: Egor Panfilov > :email:?? > :institution:?? > :equal-contributor: > :author: Alexandre de Siqueira > :email:?? > :institution: University of Campinas > :institution: TU Bergakademie Freiberg > :equal-contributor:?? > """ > We need an abstract too: > """ > scikit-image is an image processing toolbox for SciPy??which provides easy > access for segmentation, geometric transformations, color space manipulation, > analysis, filtering, morphology, feature detection, and more.??It is available?? > free of charge and restriction, and the code is written by an active??community > of volunteers. > (...) > """ > As you may see I need some ideas for that :) Since this is a cookbook, I think > it would be aimed to "recipes" using different functions/objects from the > library. Maybe we could specify some examples on the abstract. Do you have any > ideas? > I'll wait until 10hPM (Berlin time; 8hPM UTC) to submit that, so we can discuss > some ideas if you have time. > Thanks! I'm here if you need. > Kind regards, > Alex > Em quarta-feira, 31 de agosto de 2016 23:54:06 UTC+2, stefanv escreveu: > Hi Alex > On Wed, Aug 31, 2016, at 10:41, Alexandre Fioravante de Siqueira wrote: > > have you figured it out? The deadline is tomorrow, and I would really > > like to participate. > Would you please submit an initial pull request on the team's behalf? > You can add me, Egor, Emmanuelle, and anyone else who expresses interest > here as co-authors. > Emmanuelle, I will double check that the chapter is fully open when it > is done so that we can remix parts for the user guide. > Thanks > St??fan From silvertrumpet999 at gmail.com Thu Sep 1 22:45:32 2016 From: silvertrumpet999 at gmail.com (Josh Warner) Date: Thu, 1 Sep 2016 19:45:32 -0700 (PDT) Subject: Fwd: PyData Community Cookbook - August Update In-Reply-To: <1472777535.1016360.713353281.15440D94@webmail.messagingengine.com> References: <1472501613.509939.709586801.1704EAF6@webmail.messagingengine.com> <20160829204435.GC1302378@phare.normalesup.org> <1472576802.757608.710583985.061974DE@webmail.messagingengine.com> <20160830192254.GA1722536@phare.normalesup.org> <1472680444.2684150.712061369.2AC87F0C@webmail.messagingengine.com> <20160901170037.GB3064887@phare.normalesup.org> <8056474b-c088-4f75-9c5f-441f62c53c74@googlegroups.com> <1472777535.1016360.713353281.15440D94@webmail.messagingengine.com> Message-ID: I would also contribute - Joshua D. Warner, email joshua dot dale dot warner at Gmail, institution Mayo Clinic. From siqueiraaf at gmail.com Fri Sep 2 05:10:50 2016 From: siqueiraaf at gmail.com (Alexandre Fioravante de Siqueira) Date: Fri, 2 Sep 2016 02:10:50 -0700 (PDT) Subject: Fwd: PyData Community Cookbook - August Update In-Reply-To: References: <1472501613.509939.709586801.1704EAF6@webmail.messagingengine.com> <20160829204435.GC1302378@phare.normalesup.org> <1472576802.757608.710583985.061974DE@webmail.messagingengine.com> <20160830192254.GA1722536@phare.normalesup.org> <1472680444.2684150.712061369.2AC87F0C@webmail.messagingengine.com> <20160901170037.GB3064887@phare.normalesup.org> <8056474b-c088-4f75-9c5f-441f62c53c74@googlegroups.com> <1472777535.1016360.713353281.15440D94@webmail.messagingengine.com> Message-ID: Hi Josh, in which city is your Mayo Clinic unity? Thanks, Alex Em sexta-feira, 2 de setembro de 2016 04:45:32 UTC+2, Josh Warner escreveu: > > I would also contribute - Joshua D. Warner, email joshua dot dale dot > warner at Gmail, institution Mayo Clinic. -------------- next part -------------- An HTML attachment was scrubbed... URL: From multicolor.mood at gmail.com Fri Sep 2 04:54:59 2016 From: multicolor.mood at gmail.com (Egor Panfilov) Date: Fri, 2 Sep 2016 11:54:59 +0300 Subject: Task board In-Reply-To: <1472601249.1617176.710940585.4C1ED035@webmail.messagingengine.com> References: <1472501868.510757.709588497.3AE0E834@webmail.messagingengine.com> <20160829213818.GE1302378@phare.normalesup.org> <1472577988.761451.710591665.5D8E3C44@webmail.messagingengine.com> <1472601249.1617176.710940585.4C1ED035@webmail.messagingengine.com> Message-ID: Hello everyone! Here are some of mine reflections on the topic: Regarding the points raised by Stefan, I think that the main issue we have is a lack of resources and reviews (just a casual bump of https://github.com/scikit-image/scikit-image/pull/2040 here ;) ). I understand that everyone in the core team has a lot of matters to deal with outside the project, but the activity from our (maintainers) side is far less compared to the activity of the contributors. In my opinion, people tend to quit contributing and even stop using OSS if they don't have enough treatment. Of course, many of the PRs we currently have are quite poor in terms of quiality and/or abandoned (we have to be more aggressive managing them), but those which are pretty good, maybe not perfect, totally deserve to get much more attention (e.g. https://github.com/scikit-image/scikit-image/pull/1957, https://github.com/scikit-image/scikit-image/pull/1570, etc). I'd prefer to have slow (pure Python) implementations of established image processing algorithms and make more people involved in the project rather then asking them to write an extremely fast and ideal code and losing them in process. So, pt.1 - "we should do more and grow the active community". As for issues/PRs management system, I think that GitHub tags pretty much do the deal. We've recently added "status: xxx" tags to facilitate tracking of active/abandoned/WIP/review+1 issues/PRs. The only _extra_ feature I'd personally prefer to have is issues/PRs aging, so to easily observe which of them haven't gotten any activity recently. If the management system offers this kind of functionality, I'd be glad to give a shot testing it, otherwise I'm neutral about this. >From the pricing perspective, Zube is not the best choice as it offers Free plans for teams up to 4 people. I think that https://waffle.io/ could be a better alternative. Here you can see a preview https://waffle.io/scikit-image/scikit-image . From my knowledge, Waffle is one of the first services of this kind, so should be well-designed from the UI perspective. If we'd like not just to manage open GitHub issues/PRs, but have a more structured backlog for our discussions and RFCs (I'd __love__ to have RFCs, not just random discussions in issues/mailing list), Trello (trello.com) could be also a nice choice. It has awesome GitHub integration and many more features. Although, I'm not sure that devs would like to get acquainted with this heavy system just for a single project management. Pt.2 - "issues/PRs management tool for stronger management, not just for its own sake". P.S. I like the practice of `scikit-learn` guys to rename PRs as "[MRG] some awesome contribution" -> [MRG + 1] some awesome contribution". Pretty simple and cheap solution to track LGTM :+1: entities. One more point (yet it is better to start a discussion in a RFC :) ) I'd like to bring to the discussion. I remember a short discussion with Stefan, that there was a decision upon that `skimage` is a community driven-project. I understand, that it is probably mostly used for educational purposes, but we shouldn't as a project fall behind the progress in Image Processing and Computer Vision. I see that many modern Deep Learning frameworks start to implement their own image processing routines just to have a common ground for their functionality. I believe we could still catch the train. So, I propose to consider moving `skimage` infrastructure onto `theano`. That is a hell lot of work, of course, but I'm asking just for a discussion yet. >From this section, actually, one more pragmatic topic arises. Even if we keep image processing part up to the community, I think that we have to put more our (core team) efforts on the backend part of the project (not just testing and documentation part, but also e.g. make easier function chaining - https://github.com/scikit-image/scikit-image/issues/1529). I'd not expect from anyone outside the core team to have enough knowledge, experience and confidence to implement this and some other features. I.e. I believe that we have to make some necessary contributions to stay competitive. +1, In my opinion, reviewing is almost more important than writing the > code. With the current system, Github only "rewards" people who contribute > code and, I think, this is part of the problem. With every commit, people > get credit in the form of # commits or # lines of code and Github shows the > stats nicely in the profile or the project graphs. Maybe there is a way to > create an equivalent for the reviewing process, e.g., # comments and # > merged PRs. I fully agree with you, Johannes, but have not a single idea on how to implement this. Well, we still can set up a GitHub bot (sorry, I'm being unreasonably hyped by this tech these days) and track who participated in the review process for each PR, but I'm definitely not sure how fair it could be (what if I just comment something like "LOL" in 1e6 lines of code PR and got credited for that) and what kind of appreciation one might expect (like, "this person has reviewed a lot"). Ofc, we can track who put "LGTM" or "+1" on the PR page, but this isn't a fair solution either. We are already publishing "list of fame" with every new release, and an organization badge in GitHub account is self-speaking. I guess that's the most safe option we could have at the moment. Sorry for the long read. :) Have a nice we. Regards, Egor Panfilov 2016-08-31 2:54 GMT+03:00 Stefan van der Walt : > Hi Johannes > > On Tue, Aug 30, 2016, at 12:58, Johannes Sch?nberger wrote: > > I agree that Github does not provide a good overview of active/passive > > issues. I am overwhelmed by the amount of issues and, usually, after a > > week of scikit-image "abstinence" :-), I have to start from scratch to > > find the relevant issues. Tags don't really help me in this regard > > either... > > Did you look at the proposed Zube (or the alternatives)? I'd be curious > to hear what you think. > > > > We have a document (http://scikit-image.org/docs/ > stable/contribute.html) > > > that invites users to contribute, but we can simplify those > instructions > > > for newcomers, and also add a "Please help us review some code" button > > > on the front page? > > > > +1, In my opinion, reviewing is almost more important than writing the > > code. With the current system, Github only "rewards" people who > > contribute code and, I think, this is part of the problem. With every > > commit, people get credit in the form of # commits or # lines of code and > > Github shows the stats nicely in the profile or the project graphs. Maybe > > there is a way to create an equivalent for the reviewing process, e.g., # > > comments and # merged PRs. > > > > What do people think about this idea? > > We can extend our release script to pull that information from GitHub. > Would it be helpful to credit with new releases, or should this come as > more continuous feedback, e.g. a weekly mail to the list with > statistics? > > St?fan > > -- > 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+unsubscribe at googlegroups.com. > To post to this group, send an email to scikit-image at googlegroups.com. > To view this discussion on the web, visit https://groups.google.com/d/ > msgid/scikit-image/1472601249.1617176.710940585.4C1ED035% > 40webmail.messagingengine.com. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From emmanuelle.gouillart at nsup.org Fri Sep 2 08:48:11 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Fri, 2 Sep 2016 14:48:11 +0200 Subject: deep learning In-Reply-To: References: <1472501868.510757.709588497.3AE0E834@webmail.messagingengine.com> <20160829213818.GE1302378@phare.normalesup.org> <1472577988.761451.710591665.5D8E3C44@webmail.messagingengine.com> <1472601249.1617176.710940585.4C1ED035@webmail.messagingengine.com> Message-ID: <20160902124811.GA3605799@phare.normalesup.org> [changing the title of the thread since one of your comments deviated quite a lot from the topic of "task board"] > One more point (yet it is better to start a discussion in a RFC :) ) I'd like > to bring to the discussion. I remember a short discussion with Stefan, that > there was a decision upon that `skimage` is a community driven-project. I > understand, that it is probably mostly used for educational purposes, but we > shouldn't as a project fall behind the progress in Image Processing and > Computer Vision. I see that many modern Deep Learning frameworks start to > implement their own image processing routines just to have a common ground for > their functionality. I believe we could still catch the train. So, I propose to > consider moving `skimage` infrastructure onto `theano`. That is a hell lot of > work, of course, but I'm asking just for a discussion yet. > From this section, actually, one more pragmatic topic arises. Even if we keep > image processing part up to the community, I think that we have to put more our > (core team) efforts on the backend part of the project (not just testing and > documentation part, but also e.g. make easier function chaining - https:// > github.com/scikit-image/scikit-image/issues/1529). I'd not expect from anyone > outside the core team to have enough knowledge, experience and confidence to > implement this and some other features. I.e. I believe that we have to make > some necessary contributions to stay competitive. I have to say that I disagree a lot with this analysis. 1. First of all, I don't think that scikit-image is used primarily for educational purposes. If you browse through the research articles that cite the scikit-image paper, you'll find that people have used scikit-image as a building block for scientific software and applications or for research in various fields such as medical science, materials science, plant research, etc. I know several industrial groups which are using scikit-image for their daily R&D workflow. Tens of thousands of people are browsing every month through the examples of the gallery to discover how to perform specific image processing operations. That said, you're totally right to raise the question of "staying competitive". But it's a tricky issue, since in my opinion, being competitive is a subtle mixture of usability, features, performance (probably in this order, but it's a matter of debate). 2. About Deep Learning: deep learning is very cool, trendy and powerful, it can blow your mind for some operations, yet it cannot do everything in image processing. Labeling images with kittens is not the sole purpose that our users have :-). Furthermore, deep learning require intensive computations, that are best done on the GPU. Some packages like keras provide elegant solutions for deep learning and are compatible with scikit-image, thanks to the common use of numpy arrays. Can some scikit-image contributors work on a deep learning package for image processing using theano, tensorflow, keras and some of the knowledge/features of scikit-image? Probably. Does it have to be in scikit-image? I don't think so (although it could be a project of the scikit-image organization). Let's try not to build a monster package with everything and the kitchen sink, that quickly becomes uninstallable and unusable. Using theano instead of NumPy arrays would be to favor one image processing workflow at the expense of many others, so I don't think it's wise. To quote David Waley-Farley: "Yep. Theano, Numba, numexpr, Cython and PyPy shall one day all merge to form Numtron, defender of sanity, runner of fast numerics.". But before we're there, NumPy is the common denominator for the scientific packages. It would be interesting to know which are the deep learning frameworks that you're mentioning, to see how they tackle image processing. I'd be interested in knowing more about this. 3. For function chaining, it might be interesting to take a look at scikit-learn's pipeline http://scikit-learn.org/stable/modules/generated/sklearn.pipeline.Pipeline.html My 2 cents, Emma From stefanv at berkeley.edu Fri Sep 2 19:59:03 2016 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Fri, 02 Sep 2016 16:59:03 -0700 Subject: Task board In-Reply-To: References: <1472501868.510757.709588497.3AE0E834@webmail.messagingengine.com> <20160829213818.GE1302378@phare.normalesup.org> <1472577988.761451.710591665.5D8E3C44@webmail.messagingengine.com> <1472601249.1617176.710940585.4C1ED035@webmail.messagingengine.com> Message-ID: <1472860743.3255741.714392305.1F9FE56A@webmail.messagingengine.com> Hi Egor On Fri, Sep 2, 2016, at 01:54, Egor Panfilov wrote: > Regarding the points raised by Stefan, I think that the main issue we > have is a lack of resources and reviews (just a casual bump of > https://github.com/scikit-image/scikit-image/pull/2040 here ;) ). I still don't see any explanation of what the term 'l2hys' means! > I understand that everyone in the core team has a lot of matters to > deal with outside the project, but the activity from our > (maintainers) side is far less compared to the activity of the > contributors. In my opinion, people tend to quit contributing This is true, unfortunately. How do we increase the number of hours available? I can see two ways: grow the contributor community (in such a way that contributors know to review as well) or hire someone to work on the project full time. I'd be interested in exploring the latter avenue. We can also reach out to employers of existing contributors and try and negotiated dedicated working time on the project. > As for issues/PRs management system, I think that GitHub tags pretty > much do the deal. We've recently added "status: xxx" tags to > facilitate tracking of active/abandoned/WIP/review+1 issues/PRs. The issue I wanted to address was getting a good "bird's eye view" on issues. I don't think tags are that useful in that regard. > From the pricing perspective, Zube is not the best choice as it offers > Free plans for teams up to 4 people. I think No, Zube is free for open source, for unlimited users. > (I'd __love__ to have RFCs, not just random discussions in > issues/mailing list), Trello (trello.com) could be also a nice choice. You mean RFCs like PEPs? > Pt.2 - "issues/PRs management tool for stronger management, not just > for its own sake". > P.S. I like the practice of `scikit-learn` guys to rename PRs as > "[MRG] some awesome contribution" -> [MRG + 1] some awesome > contribution". Pretty simple and cheap solution to track LGTM > :+1: entities. I'd be fine with that. > outines just to have a common ground for their functionality. I > believe we could still catch the train. So, I propose to consider > moving `skimage` infrastructure onto `theano`. That is a hell lot of > work, of course, but I'm asking just for a discussion yet. We do evaluate these things from time to time. When GPUs came into fashion, we looked at those, at a recent conference I spoke to folks about using DSLs like Halide for speed optimization, and with our GSoC student Daniil we've spoken a lot about integrating neural nets. Adopting theano may be quite tricky, so perhaps a proof of concept (or an RFC ;) would be the easiest way to kick off that conversation. > From this section, actually, one more pragmatic topic arises. Even if > we keep image processing part up to the community, I think that we > have to put more our (core team) efforts on the backend part of the > project (not just testing and documentation part, but also e.g. make > easier function chaining - > https://github.com/scikit-image/scikit-image/issues/1529). I'd not > expect from anyone outside the core team to have enough knowledge, > experience and confidence to implement this and some other features. > I.e. I believe that we have to make some necessary contributions to > stay competitive. Can you explain what you mean? Thanks for all your comments, St?fan -------------- next part -------------- An HTML attachment was scrubbed... URL: From silvertrumpet999 at gmail.com Fri Sep 2 20:49:24 2016 From: silvertrumpet999 at gmail.com (Josh Warner) Date: Fri, 2 Sep 2016 17:49:24 -0700 (PDT) Subject: Fwd: PyData Community Cookbook - August Update In-Reply-To: References: <1472501613.509939.709586801.1704EAF6@webmail.messagingengine.com> <20160829204435.GC1302378@phare.normalesup.org> <1472576802.757608.710583985.061974DE@webmail.messagingengine.com> <20160830192254.GA1722536@phare.normalesup.org> <1472680444.2684150.712061369.2AC87F0C@webmail.messagingengine.com> <20160901170037.GB3064887@phare.normalesup.org> <8056474b-c088-4f75-9c5f-441f62c53c74@googlegroups.com> <1472777535.1016360.713353281.15440D94@webmail.messagingengine.com> Message-ID: Rochester, Minnesota. From jsch at demuc.de Sat Sep 3 05:32:06 2016 From: jsch at demuc.de (=?utf-8?Q?Johannes_Sch=C3=B6nberger?=) Date: Sat, 3 Sep 2016 11:32:06 +0200 Subject: Task board In-Reply-To: <1472860743.3255741.714392305.1F9FE56A@webmail.messagingengine.com> References: <1472501868.510757.709588497.3AE0E834@webmail.messagingengine.com> <20160829213818.GE1302378@phare.normalesup.org> <1472577988.761451.710591665.5D8E3C44@webmail.messagingengine.com> <1472601249.1617176.710940585.4C1ED035@webmail.messagingengine.com> <1472860743.3255741.714392305.1F9FE56A@webmail.messagingengine.com> Message-ID: <6A1A0B3B-7F3A-4026-A83A-D70803681E2F@demuc.de> Hi, >> I understand that everyone in the core team has a lot of matters to deal with outside the project, but the activity from our (maintainers) side is far less compared to the activity of the contributors. In my opinion, people tend to quit contributing > > This is true, unfortunately. How do we increase the number of hours available? I can see two ways: grow the contributor community (in such a way that contributors know to review as well) or hire someone to work on the project full time. I'd be interested in exploring the latter avenue. We can also reach out to employers of existing contributors and try and negotiated dedicated working time on the project. The latter would be a great step forward! >> Pt.2 - "issues/PRs management tool for stronger management, not just for its own sake". >> P.S. I like the practice of `scikit-learn` guys to rename PRs as "[MRG] some awesome contribution" -> [MRG + 1] some awesome contribution". Pretty simple and cheap solution to track LGTM :+1: entities. > > I'd be fine with that. +1 >> outines just to have a common ground for their functionality. I believe we could still catch the train. So, I propose to consider moving `skimage` infrastructure onto `theano`. That is a hell lot of work, of course, but I'm asking just for a discussion yet. > > We do evaluate these things from time to time. When GPUs came into fashion, we looked at those, at a recent conference I spoke to folks about using DSLs like Halide for speed optimization, and with our GSoC student Daniil we've spoken a lot about integrating neural nets. Adopting theano may be quite tricky, so perhaps a proof of concept (or an RFC ;) would be the easiest way to kick off that conversation. I'd argue that scikit-image wouldn't gain any more traction by transitioning to Theano. The big advantage of theano in the deep learning setting is its automatic differentiation functionality. This will only be useful for a very small subset of functions in scikit-image. The input/output variables to any Python-based deep learning framework are still numpy arrays. >> From this section, actually, one more pragmatic topic arises. Even if we keep image processing part up to the community, I think that we have to put more our (core team) efforts on the backend part of the project (not just testing and documentation part, but also e.g. make easier function chaining - https://github.com/scikit-image/scikit-image/issues/1529). I'd not expect from anyone outside the core team to have enough knowledge, experience and confidence to implement this and some other features. I.e. I believe that we have to make some necessary contributions to stay competitive. It would be good, if you could elaborate a little more on this point. Most of skimage's API was designed with exactly that in mind. Best, Johannes From jsch at demuc.de Sun Sep 4 04:46:28 2016 From: jsch at demuc.de (=?utf-8?Q?Johannes_Sch=C3=B6nberger?=) Date: Sun, 4 Sep 2016 10:46:28 +0200 Subject: Task board In-Reply-To: References: <1472501868.510757.709588497.3AE0E834@webmail.messagingengine.com> <20160829213818.GE1302378@phare.normalesup.org> <1472577988.761451.710591665.5D8E3C44@webmail.messagingengine.com> <1472601249.1617176.710940585.4C1ED035@webmail.messagingengine.com> <1472860743.3255741.714392305.1F9FE56A@webmail.messagingengine.com> Message-ID: <4225E36F-E22C-4C76-9C8E-EC7B24B21F13@demuc.de> To better keep track of PR/issues, I suggest core developers assign themselves to some of the issues in their field of expertise. There are so many PRs that are >90% finished but it seems we forgot to continue reviewing them. > On Sep 4, 2016, at 10:32 AM, Egor Panfilov wrote: > > Hi Stefan! > >> As for issues/PRs management system, I think that GitHub tags pretty much do the deal. We've recently added "status: xxx" tags to facilitate tracking of active/abandoned/WIP/review+1 issues/PRs. > The issue I wanted to address was getting a good "bird's eye view" on issues. I don't think tags are that useful in that regard. > > Yes, I see. I think, this could be helpful for project owners to make strategic decisions. On the other hand, I personally don't find a great benefit of using these tools for triaging, cross-linking issues/PRs and other cases I care about. Maybe we should just give it a try. >> From the pricing perspective, Zube is not the best choice as it offers Free plans for teams up to 4 people. I think > No, Zube is free for open source, for unlimited users. > > Indeed, sorry, I see this now. >> (I'd __love__ to have RFCs, not just random discussions in issues/mailing list), Trello (trello.com) could be also a nice choice. > You mean RFCs like PEPs? > > Exactly. I think, this format would help to accumulate our opinions on different matters (e.g. how to we treat and depend on `matplotlib`), for which website (deeply buried pages of it) is not the best place. At the moment, discussions on many sensitive topics appear again and again in the different PRs, making them hard to align and to be referenced. > As for technical side of this, we probably could reuse GitHub issues (by creating exclusive tag "SkimageEP" or something similar). `matplotlib` people, as far as I know, use GitHub Wiki to post "xEP"s, but I'm not sure where do they held the discusssions. GitHub does also support protecting different pages from modifcation, that could also be useful. >> From this section, actually, one more pragmatic topic arises. Even if we keep image processing part up to the community, I think that we have to put more our (core team) efforts on the backend part of the project (not just testing and documentation part, but also e.g. make easier function chaining - https://github.com/scikit-image/scikit-image/issues/1529). I'd not expect from anyone outside the core team to have enough knowledge, experience and confidence to implement this and some other features. I.e. I believe that we have to make some necessary contributions to stay competitive. > Can you explain what you mean? > > Well, I'm just saying that we as a core team should drive the evolution of backend and make life easier for contributors and users. Like, try to imagine some new contributor making a PR introducing Sphinx Gallery. Can't see this happenning. Of course, all of us are working on this kind of features already, I just want to highlight this (maybe trivial) point. > As a "practical guide", perhaps we should dedicate more time to the _complex_ issues/requests/PRs we have. > > > Thanks for all your comments on Theano/GPU/whatever part (/cc Emmanuelle, Johannes), they're very informative and insightful. I'd prefer to raise this discussion again (as I have more food to bring to the table) or maybe just collect your opinions in one place when (and if) we decipe on SkimageEPs. > > Regards, > Egor > > -- > 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+unsubscribe at googlegroups.com. > To post to this group, send email to scikit-image at googlegroups.com. > To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/CAP0v5tm5C4%3Df9c9u1juf37yYpXipkZU%3Ds1zwVO5GMikqnB2KVQ%40mail.gmail.com. > For more options, visit https://groups.google.com/d/optout. From emmanuelle.gouillart at nsup.org Sun Sep 4 04:51:22 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Sun, 4 Sep 2016 10:51:22 +0200 Subject: Task board In-Reply-To: <4225E36F-E22C-4C76-9C8E-EC7B24B21F13@demuc.de> References: <1472501868.510757.709588497.3AE0E834@webmail.messagingengine.com> <20160829213818.GE1302378@phare.normalesup.org> <1472577988.761451.710591665.5D8E3C44@webmail.messagingengine.com> <1472601249.1617176.710940585.4C1ED035@webmail.messagingengine.com> <1472860743.3255741.714392305.1F9FE56A@webmail.messagingengine.com> <4225E36F-E22C-4C76-9C8E-EC7B24B21F13@demuc.de> Message-ID: <20160904085122.GA309739@phare.normalesup.org> On Sun, Sep 04, 2016 at 10:46:28AM +0200, Johannes Sch??nberger wrote: > To better keep track of PR/issues, I suggest core developers assign themselves to some of the issues in their field of expertise. There are so many PRs that are >90% finished but it seems we forgot to continue reviewing them. Yes, and we can also tentatively assign someone else if we feel that a given PR is in his/her realm of expertise. If the other person disagrees, it's always possible to un-assign oneself :-). From jsch at demuc.de Sun Sep 4 04:55:58 2016 From: jsch at demuc.de (=?utf-8?Q?Johannes_Sch=C3=B6nberger?=) Date: Sun, 4 Sep 2016 10:55:58 +0200 Subject: Task board In-Reply-To: <20160904085122.GA309739@phare.normalesup.org> References: <1472501868.510757.709588497.3AE0E834@webmail.messagingengine.com> <20160829213818.GE1302378@phare.normalesup.org> <1472577988.761451.710591665.5D8E3C44@webmail.messagingengine.com> <1472601249.1617176.710940585.4C1ED035@webmail.messagingengine.com> <1472860743.3255741.714392305.1F9FE56A@webmail.messagingengine.com> <4225E36F-E22C-4C76-9C8E-EC7B24B21F13@demuc.de> <20160904085122.GA309739@phare.normalesup.org> Message-ID: <472796D6-3B53-49AE-A8B7-82F550A64F93@demuc.de> >> To better keep track of PR/issues, I suggest core developers assign themselves to some of the issues in their field of expertise. There are so many PRs that are >90% finished but it seems we forgot to continue reviewing them. > > Yes, and we can also tentatively assign someone else if we feel that a > given PR is in his/her realm of expertise. If the other person disagrees, > it's always possible to un-assign oneself :-). Fully agreed and I already went ahead and did so for https://github.com/scikit-image/scikit-image/pull/1884 :-) > > -- > 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+unsubscribe at googlegroups.com. > To post to this group, send an email to scikit-image at googlegroups.com. > To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/20160904085122.GA309739%40phare.normalesup.org. > For more options, visit https://groups.google.com/d/optout. From multicolor.mood at gmail.com Sun Sep 4 04:32:20 2016 From: multicolor.mood at gmail.com (Egor Panfilov) Date: Sun, 4 Sep 2016 11:32:20 +0300 Subject: Task board In-Reply-To: <1472860743.3255741.714392305.1F9FE56A@webmail.messagingengine.com> References: <1472501868.510757.709588497.3AE0E834@webmail.messagingengine.com> <20160829213818.GE1302378@phare.normalesup.org> <1472577988.761451.710591665.5D8E3C44@webmail.messagingengine.com> <1472601249.1617176.710940585.4C1ED035@webmail.messagingengine.com> <1472860743.3255741.714392305.1F9FE56A@webmail.messagingengine.com> Message-ID: Hi Stefan! As for issues/PRs management system, I think that GitHub tags pretty much > do the deal. We've recently added "status: xxx" tags to facilitate tracking > of active/abandoned/WIP/review+1 issues/PRs. > > The issue I wanted to address was getting a good "bird's eye view" on > issues. I don't think tags are that useful in that regard. > Yes, I see. I think, this could be helpful for project owners to make strategic decisions. On the other hand, I personally don't find a great benefit of using these tools for triaging, cross-linking issues/PRs and other cases I care about. Maybe we should just give it a try. > From the pricing perspective, Zube is not the best choice as it offers > Free plans for teams up to 4 people. I think > > No, Zube is free for open source, for unlimited users. > Indeed, sorry, I see this now. > (I'd __love__ to have RFCs, not just random discussions in issues/mailing > list), Trello (trello.com) could be also a nice choice. > > You mean RFCs like PEPs? > Exactly. I think, this format would help to accumulate our opinions on different matters (e.g. how to we treat and depend on `matplotlib`), for which website (deeply buried pages of it) is not the best place. At the moment, discussions on many sensitive topics appear again and again in the different PRs, making them hard to align and to be referenced. As for technical side of this, we probably could reuse GitHub issues (by creating exclusive tag "SkimageEP" or something similar). `matplotlib` people, as far as I know, use GitHub Wiki to post "xEP"s, but I'm not sure where do they held the discusssions. GitHub does also support protecting different pages from modifcation, that could also be useful. > From this section, actually, one more pragmatic topic arises. Even if we > keep image processing part up to the community, I think that we have to put > more our (core team) efforts on the backend part of the project (not just > testing and documentation part, but also e.g. make easier function chaining > - https://github.com/scikit-image/scikit-image/issues/1529). I'd not > expect from anyone outside the core team to have enough knowledge, > experience and confidence to implement this and some other features. I.e. I > believe that we have to make some necessary contributions to stay > competitive. > > Can you explain what you mean? > > Well, I'm just saying that we as a core team should drive the evolution of backend and make life easier for contributors and users. Like, try to imagine some new contributor making a PR introducing Sphinx Gallery. Can't see this happenning. Of course, all of us are working on this kind of features already, I just want to highlight this (maybe trivial) point. As a "practical guide", perhaps we should dedicate more time to the _complex_ issues/requests/PRs we have. Thanks for all your comments on Theano/GPU/whatever part (/cc Emmanuelle, Johannes), they're very informative and insightful. I'd prefer to raise this discussion again (as I have more food to bring to the table) or maybe just collect your opinions in one place when (and if) we decipe on SkimageEPs. Regards, Egor -------------- next part -------------- An HTML attachment was scrubbed... URL: From siqueiraaf at gmail.com Mon Sep 5 01:16:04 2016 From: siqueiraaf at gmail.com (Alexandre Fioravante de Siqueira) Date: Sun, 4 Sep 2016 22:16:04 -0700 (PDT) Subject: Fwd: PyData Community Cookbook - August Update In-Reply-To: References: <1472501613.509939.709586801.1704EAF6@webmail.messagingengine.com> <20160829204435.GC1302378@phare.normalesup.org> <1472576802.757608.710583985.061974DE@webmail.messagingengine.com> <20160830192254.GA1722536@phare.normalesup.org> <1472680444.2684150.712061369.2AC87F0C@webmail.messagingengine.com> <20160901170037.GB3064887@phare.normalesup.org> <8056474b-c088-4f75-9c5f-441f62c53c74@googlegroups.com> <1472777535.1016360.713353281.15440D94@webmail.messagingengine.com> Message-ID: Thanks. Already pushed. Em s?bado, 3 de setembro de 2016 02:49:24 UTC+2, Josh Warner escreveu: > > Rochester, Minnesota. -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Mon Sep 5 06:42:46 2016 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Mon, 05 Sep 2016 03:42:46 -0700 Subject: Task board In-Reply-To: References: <1472501868.510757.709588497.3AE0E834@webmail.messagingengine.com> <20160829213818.GE1302378@phare.normalesup.org> <1472577988.761451.710591665.5D8E3C44@webmail.messagingengine.com> <1472601249.1617176.710940585.4C1ED035@webmail.messagingengine.com> <1472860743.3255741.714392305.1F9FE56A@webmail.messagingengine.com> Message-ID: <1473072166.3811302.715986121.25BB7976@webmail.messagingengine.com> On Sun, Sep 4, 2016, at 01:32, Egor Panfilov wrote: >> You mean RFCs like PEPs? > > Exactly. I think, this format would help to accumulate our opinions on > different matters (e.g. how to we treat and depend on `matplotlib`) We should chat to Ralf Gommers to find out how successful the Enhancement Proposal approach has been for SciPy, which is similar to this project in many ways. > Well, I'm just saying that we as a core team should drive the > evolution of backend and make life easier for contributors and users. > Like, try to imagine some new contributor making a PR introducing > Sphinx Gallery. Can't see this happenning. Of course, all of us are > working on this kind of features already, I just want to highlight > this (maybe trivial) point. > As a "practical guide", perhaps we should dedicate more time to the > _complex_ issues/requests/PRs we have. Still, I'm unclear how we can make it easier for newcomers to contribute to the backend. Do you have any practical suggestions? Best regards Stefan -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Mon Sep 5 16:05:40 2016 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Tue, 6 Sep 2016 08:05:40 +1200 Subject: Task board In-Reply-To: <1473072166.3811302.715986121.25BB7976@webmail.messagingengine.com> References: <1472501868.510757.709588497.3AE0E834@webmail.messagingengine.com> <20160829213818.GE1302378@phare.normalesup.org> <1472577988.761451.710591665.5D8E3C44@webmail.messagingengine.com> <1472601249.1617176.710940585.4C1ED035@webmail.messagingengine.com> <1472860743.3255741.714392305.1F9FE56A@webmail.messagingengine.com> <1473072166.3811302.715986121.25BB7976@webmail.messagingengine.com> Message-ID: On Mon, Sep 5, 2016 at 10:42 PM, Stefan van der Walt wrote: > On Sun, Sep 4, 2016, at 01:32, Egor Panfilov wrote: > > You mean RFCs like PEPs? > > > Exactly. I think, this format would help to accumulate our opinions on > different matters (e.g. how to we treat and depend on `matplotlib`) > > > We should chat to Ralf Gommers to find out how successful the Enhancement > Proposal approach has been for SciPy, which is similar to this project in > many ways. > Since we don't have those for SciPy, I'd say not very:) You're thinking about NumPy probably: http://docs.scipy.org/doc/numpy/neps/index.html https://github.com/numpy/numpy/tree/master/doc/neps We don't use them often, but when we do they've been valuable. For example the .npy version format is a good reference with rationale, and for complex discussions like datetime and NA it helps to summarize the issues and outlike solution directions (emails really don't work well for that). Cheers, Ralf -------------- next part -------------- An HTML attachment was scrubbed... URL: From multicolor.mood at gmail.com Thu Sep 8 10:22:14 2016 From: multicolor.mood at gmail.com (Egor Panfilov) Date: Thu, 8 Sep 2016 07:22:14 -0700 (PDT) Subject: Management of PRs, issues, and threads In-Reply-To: <20160822212651.GC1708463@phare.normalesup.org> References: <20160822212651.GC1708463@phare.normalesup.org> Message-ID: <652668af-4e70-4222-8357-552edea1675e@googlegroups.com> Hi everyone! Remember me hyping around with the GitHub bot idea? Here it is: - in the source code: https://github.com/facebook/mention-bot - in action: https://github.com/tensorflow/tensorflow/pull/4239#issuecomment-245180925 Just putting it here to bookmark. If someone of you will decide to play with it, I'm all ears to hear the feedback. I'll most likely give it a try in the coming weeks. Regards, Egor ???????, 23 ??????? 2016 ?., 0:26:52 UTC+3 ???????????? Emmanuelle Gouillart ???????: > > Hi Juan, > > thanks for bringing these issues to light. How about we tackle the queue > of open PRs from its two ends? That is, for the new PRs we have this > manager system (we still need to decide how to assign them), and at the > same time we go through old PRs to try to unblock or (worst case) close > them? > > Best, > Emma > > On Mon, Aug 22, 2016 at 02:47:16PM +1000, Juan Nunez-Iglesias wrote: > > Hi everyone, > > > We've had a couple of community fails on GitHub recently: > > > https://github.com/scikit-image/scikit-image/pull/1474#issuecomment-241283056 > > https://github.com/scikit-image/scikit-image/issues/2080 > > (The last one is missing a presumably-deleted comment where someone > outside the > > project recommended to a potential contributor to just fork the > project!). > > > That's just the couple I've noticed, I'm sure there are lots more. We > > definitely have many, many abandoned PRs from >1y, >2y ago. > > > Obviously, something in our process isn't working. I don't have > immediate > > solutions, but here's a couple of suggestions: > > > - we need a system to assign core devs to PRs/issues. Currently, it's > too easy > > for all of us to go, "someone else on the team will handle this". We > need a > > fair way to assign a manager to each issue/PR. The assigned dev wouldn't > > necessarily be responsible for review, but they would be responsible for > > chasing up other reviewers. > > > - NEVER close a PR without the explicit consent of the contributor, OR > after > > the contributor has been non-responsive for e.g. 1mo and two pings. In > this > > last situation I would even suggest that we need two core devs to sign > off. > > > Other suggestions welcome in this thread. We should try to get a new > process > > hammered out very soon. > > > I also want to acknowledge @soupault for his triage/labelling work, > which is a > > massive step in the right direction. But we need to follow up his triage > with > > some actual process. > > > Juan. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Sat Sep 10 03:21:59 2016 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Sat, 10 Sep 2016 00:21:59 -0700 Subject: Management of PRs, issues, and threads In-Reply-To: <652668af-4e70-4222-8357-552edea1675e@googlegroups.com> References: <20160822212651.GC1708463@phare.normalesup.org> <652668af-4e70-4222-8357-552edea1675e@googlegroups.com> Message-ID: <1473492119.3186673.721418913.0D959363@webmail.messagingengine.com> On Thu, Sep 8, 2016, at 07:22, Egor Panfilov wrote: > Remember me hyping around with the GitHub bot idea? > Here it is: > - in the source code: https://github.com/facebook/mention-bot > - in action: > https://github.com/tensorflow/tensorflow/pull/4239#issuecomment-245180925 This is cute. Although I think what could be even more useful is a feature I saw elsewhere: instead of clicking the merge button, you instruct it to re-run the test suite and merge upon successful completion. This way your PRs are always checked against latest master, not whatever was around when they were first made. St?fan -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew.brett at gmail.com Sat Sep 10 03:32:21 2016 From: matthew.brett at gmail.com (Matthew Brett) Date: Sat, 10 Sep 2016 00:32:21 -0700 Subject: Management of PRs, issues, and threads In-Reply-To: <1473492119.3186673.721418913.0D959363@webmail.messagingengine.com> References: <20160822212651.GC1708463@phare.normalesup.org> <652668af-4e70-4222-8357-552edea1675e@googlegroups.com> <1473492119.3186673.721418913.0D959363@webmail.messagingengine.com> Message-ID: Hi, On Sat, Sep 10, 2016 at 12:21 AM, Stefan van der Walt wrote: > On Thu, Sep 8, 2016, at 07:22, Egor Panfilov wrote: > > Remember me hyping around with the GitHub bot idea? > Here it is: > - in the source code: https://github.com/facebook/mention-bot > - in action: > https://github.com/tensorflow/tensorflow/pull/4239#issuecomment-245180925 > > > This is cute. Although I think what could be even more useful is a feature > I saw elsewhere: instead of clicking the merge button, you instruct it to > re-run the test suite and merge upon successful completion. This way your > PRs are always checked against latest master, not whatever was around when > they were first made. Yes, this was the homu bot - we have a copy of that running on the nipy server in Berkeley. Matthias B of IPython fame was talking about sharing some work to refactor the homu code into something more general to extend the range of github tasks it could do - maybe including mention-automation like the face-book-bot. Matthew From multicolor.mood at gmail.com Sat Sep 10 04:43:35 2016 From: multicolor.mood at gmail.com (Egor Panfilov) Date: Sat, 10 Sep 2016 11:43:35 +0300 Subject: Management of PRs, issues, and threads In-Reply-To: References: <20160822212651.GC1708463@phare.normalesup.org> <652668af-4e70-4222-8357-552edea1675e@googlegroups.com> <1473492119.3186673.721418913.0D959363@webmail.messagingengine.com> Message-ID: Dears, I believe there might be a generic solution already: see my comment ( https://github.com/scikit-image/scikit-image/issues/2269#issuecomment-243357010) and, particularly, "rust-lang" reference. Regards, Egor 2016-09-10 10:32 GMT+03:00 Matthew Brett : > Hi, > > On Sat, Sep 10, 2016 at 12:21 AM, Stefan van der Walt > wrote: > > On Thu, Sep 8, 2016, at 07:22, Egor Panfilov wrote: > > > > Remember me hyping around with the GitHub bot idea? > > Here it is: > > - in the source code: https://github.com/facebook/mention-bot > > - in action: > > https://github.com/tensorflow/tensorflow/pull/4239# > issuecomment-245180925 > > > > > > This is cute. Although I think what could be even more useful is a > feature > > I saw elsewhere: instead of clicking the merge button, you instruct it to > > re-run the test suite and merge upon successful completion. This way > your > > PRs are always checked against latest master, not whatever was around > when > > they were first made. > > Yes, this was the homu bot - we have a copy of that running on the > nipy server in Berkeley. Matthias B of IPython fame was talking > about sharing some work to refactor the homu code into something more > general to extend the range of github tasks it could do - maybe > including mention-automation like the face-book-bot. > > Matthew > > -- > 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+unsubscribe at googlegroups.com. > To post to this group, send an email to scikit-image at googlegroups.com. > To view this discussion on the web, visit https://groups.google.com/d/ > msgid/scikit-image/CAH6Pt5phve%3DS1t1haAVT%3D3% > 3DRhwwDBdZzO9Mqh1ED4_cDx2B-Pw%40mail.gmail.com. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Mon Sep 12 02:13:29 2016 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Mon, 12 Sep 2016 02:13:29 -0400 Subject: Management of PRs, issues, and threads In-Reply-To: References: <20160822212651.GC1708463@phare.normalesup.org> <652668af-4e70-4222-8357-552edea1675e@googlegroups.com> <1473492119.3186673.721418913.0D959363@webmail.messagingengine.com> Message-ID: > This way your PRs are always checked against the latest master, not whatever was around when they were first made I thought Travis did this already? https://docs.travis-ci.com/user/pull-requests "Rather than test the commits that have been pushed to the branch the pull request is from, we test the merge between the origin and the upstream branch." However this would imply that Travis wouldn't do anything when you can't automatically merge. I don't remember whether this is True... On 10 September 2016 at 5:33:04 PM, Matthew Brett (matthew.brett at gmail.com) wrote: Hi, On Sat, Sep 10, 2016 at 12:21 AM, Stefan van der Walt wrote: > On Thu, Sep 8, 2016, at 07:22, Egor Panfilov wrote: > > Remember me hyping around with the GitHub bot idea? > Here it is: > - in the source code: https://github.com/facebook/mention-bot > - in action: > https://github.com/tensorflow/tensorflow/pull/4239#issuecomment-245180925 > > > This is cute. Although I think what could be even more useful is a feature > I saw elsewhere: instead of clicking the merge button, you instruct it to > re-run the test suite and merge upon successful completion. This way your > PRs are always checked against latest master, not whatever was around when > they were first made. Yes, this was the homu bot - we have a copy of that running on the nipy server in Berkeley. Matthias B of IPython fame was talking about sharing some work to refactor the homu code into something more general to extend the range of github tasks it could do - maybe including mention-automation like the face-book-bot. Matthew -- 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+unsubscribe at googlegroups.com. To post to this group, send an email to scikit-image at googlegroups.com. To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/CAH6Pt5phve%3DS1t1haAVT%3D3%3DRhwwDBdZzO9Mqh1ED4_cDx2B-Pw%40mail.gmail.com. For more options, visit https://groups.google.com/d/optout. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nelle.varoquaux at gmail.com Mon Sep 12 12:35:03 2016 From: nelle.varoquaux at gmail.com (Nelle Varoquaux) Date: Mon, 12 Sep 2016 09:35:03 -0700 Subject: Management of PRs, issues, and threads In-Reply-To: References: Message-ID: Hi scikit-image folks! > We've had a couple of community fails on GitHub recently: > https://github.com/scikit-image/scikit-image/pull/1474#issuecomment-241283056 > https://github.com/scikit-image/scikit-image/issues/2080 > (The last one is missing a presumably-deleted comment where someone outside > the project recommended to a potential contributor to just fork the > project!). Being the person that reported one of those community fails, I'd like to say that I've had great experience with the scikit-image community overall. Contributors are (usually) very well welcomed, feedback is friendly, and we can have discussion and debates about "hot" topics (like dropping python2.7) in a friendly and nice environment. I've recently contributed to another scientific python project where many members of the community were aggressive in their reviews, without giving valuable feedback on PRs, so I value scikit-image's (& scikit-learn) community even more. > That's just the couple I've noticed, I'm sure there are lots more. We > definitely have many, many abandoned PRs from >1y, >2y ago. > > Obviously, something in our process isn't working. I don't have immediate > solutions, but here's a couple of suggestions: > > - we need a system to assign core devs to PRs/issues. Currently, it's too > easy for all of us to go, "someone else on the team will handle this". We > need a fair way to assign a manager to each issue/PR. The assigned dev > wouldn't necessarily be responsible for review, but they would be > responsible for chasing up other reviewers. > > - NEVER close a PR without the explicit consent of the contributor, OR after > the contributor has been non-responsive for e.g. 1mo and two pings. In this > last situation I would even suggest that we need two core devs to sign off. I would not close old PR, for the sake of closing them. If the contributor is not interested in finishing the contribution and the patch is almost ready, it might be a good way to introduce new contributors (/students) to the PR. This can probably be done by an "Need contributor" tag + "Easy fix", though I haven't thought more about this > Other suggestions welcome in this thread. We should try to get a new process > hammered out very soon. > > I also want to acknowledge @soupault for his triage/labelling work, which is > a massive step in the right direction. But we need to follow up his triage > with some actual process. > > Juan. > > -- > 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+unsubscribe at googlegroups.com. > To post to this group, send email to scikit-image at googlegroups.com. > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/CA%2BJHcKSh-k%2ByM0yBTRzTy%3DZgY7%2BOoEmPkKNA4xUgudeyhCJ5Dw%40mail.gmail.com. > For more options, visit https://groups.google.com/d/optout. From siqueiraaf at gmail.com Wed Sep 14 09:20:40 2016 From: siqueiraaf at gmail.com (Alexandre Fioravante de Siqueira) Date: Wed, 14 Sep 2016 06:20:40 -0700 (PDT) Subject: Fwd: PyData Community Cookbook - August Update In-Reply-To: <20160901170037.GB3064887@phare.normalesup.org> References: <1472501613.509939.709586801.1704EAF6@webmail.messagingengine.com> <20160829204435.GC1302378@phare.normalesup.org> <1472576802.757608.710583985.061974DE@webmail.messagingengine.com> <20160830192254.GA1722536@phare.normalesup.org> <1472680444.2684150.712061369.2AC87F0C@webmail.messagingengine.com> <20160901170037.GB3064887@phare.normalesup.org> Message-ID: Hi all, like Emmanuelle said in this previous e-mail, it's time to think about the content. Would you like to point any gallery examples for that? What do you think it's important to be in that chapter? I was thinking on a first section about the basics: open a file, separate the color channels, present histograms, all that stuff. Thanks. Looking forward to work with you, Alex Em quinta-feira, 1 de setembro de 2016 19:00:40 UTC+2, Emmanuelle Gouillart escreveu: > > ... it's a good time to start thinking about the content. Even if it's > advertised as a "cookbook", I think that a length of 15-20 pages is > enough to present both "recipes" and also some big picture stuff (why and > when use scikit-image or other image processing libraries? what are the > typical coding patterns? etc.). As for the recipes, if we can re-use some > of our gallery examples it will save us some precious time. How about we > select one example if each of the chapters of the gallery and we take > advantage of the cookbook to improve it? > > Best, > Emma > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jalopcar at gmail.com Wed Sep 14 17:29:30 2016 From: jalopcar at gmail.com (Jaime Lopez Carvajal) Date: Wed, 14 Sep 2016 14:29:30 -0700 (PDT) Subject: neighbors contour length Message-ID: <191cefe6-7274-45f7-b266-41bb92d64428@googlegroups.com> Hi, I would like to know if someone could help or suggest any idea how to do this: First, I am trying to know how many neighbors (objects) one particular object have using its contour. Second, I need to extract the length of each shared contour with every neighbor, Third, calculate their respective percentage. The last step is the easiest, but I dont know how to get the first and second steps. Example using attached image: Object of interest: red object Neighbors: three neighbors with three shared contours (yellow, green and blue). Total length contour = lengh(yellow) + lengh(yellow) + lengh(yellow) Any suggestion how can I get this? Thanks in advance, Jaime -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: object_neighbors.jpg Type: image/jpeg Size: 7774 bytes Desc: not available URL: From stefanv at berkeley.edu Wed Sep 14 19:08:53 2016 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Wed, 14 Sep 2016 16:08:53 -0700 Subject: Task board In-Reply-To: <1472501868.510757.709588497.3AE0E834@webmail.messagingengine.com> References: <1472501868.510757.709588497.3AE0E834@webmail.messagingengine.com> Message-ID: <1473894533.1455710.726083169.1D4C654B@webmail.messagingengine.com> On Mon, Aug 29, 2016, at 13:17, Stefan van der Walt wrote: > I have some ideas around (1) that need fleshing out, but in the mean > time I was looking at http://zube.io to address part of (2). Take a look at this! https://github.com/blog/2256-a-whole-new-github-universe-announcing-new-tools-forums-and-features E.g., here's an empty project to play around with: https://github.com/scikit-image/scikit-image/projects/1 St?fan From stefanv at berkeley.edu Wed Sep 14 19:25:09 2016 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Wed, 14 Sep 2016 16:25:09 -0700 Subject: Management of PRs, issues, and threads In-Reply-To: References: <20160822212651.GC1708463@phare.normalesup.org> <652668af-4e70-4222-8357-552edea1675e@googlegroups.com> <1473492119.3186673.721418913.0D959363@webmail.messagingengine.com> Message-ID: <1473895509.1458211.726097937.57B30309@webmail.messagingengine.com> On Sun, Sep 11, 2016, at 23:13, Juan Nunez-Iglesias wrote: > > This way your PRs are always checked against the latest master, not > > whatever was around when they were first made > > I thought Travis did this already? > > https://docs.travis-ci.com/user/pull-requests > > "Rather than test the commits that have been pushed to the branch the > pull request is from, we test the merge between the origin and the > upstream branch." This happens the moment you make the PR, or push new commits. Ideally, you want to run the tests just before merging. St?fan -------------- next part -------------- An HTML attachment was scrubbed... URL: From jsch at demuc.de Wed Sep 14 14:33:12 2016 From: jsch at demuc.de (=?utf-8?Q?Johannes_Sch=C3=B6nberger?=) Date: Wed, 14 Sep 2016 20:33:12 +0200 Subject: Management of PRs, issues, and threads In-Reply-To: References: Message-ID: <4440C15B-2192-4BEC-83FF-12B7A9CF6430@demuc.de> This should very be interesting in this regard: https://github.com/blog/2256-a-whole-new-github-universe-announcing-new-tools-forums-and-features > On 12 Sep 2016, at 18:35, Nelle Varoquaux wrote: > > Hi scikit-image folks! > > >> We've had a couple of community fails on GitHub recently: >> https://github.com/scikit-image/scikit-image/pull/1474#issuecomment-241283056 >> https://github.com/scikit-image/scikit-image/issues/2080 >> (The last one is missing a presumably-deleted comment where someone outside >> the project recommended to a potential contributor to just fork the >> project!). > > Being the person that reported one of those community fails, I'd like > to say that I've had great experience with the scikit-image community > overall. Contributors are (usually) very well welcomed, feedback is > friendly, and we can have discussion and debates about "hot" topics > (like dropping python2.7) in a friendly and nice environment. I've > recently contributed to another scientific python project where many > members of the community were aggressive in their reviews, without > giving valuable feedback on PRs, so I value scikit-image's (& > scikit-learn) community even more. > >> That's just the couple I've noticed, I'm sure there are lots more. We >> definitely have many, many abandoned PRs from >1y, >2y ago. >> >> Obviously, something in our process isn't working. I don't have immediate >> solutions, but here's a couple of suggestions: >> >> - we need a system to assign core devs to PRs/issues. Currently, it's too >> easy for all of us to go, "someone else on the team will handle this". We >> need a fair way to assign a manager to each issue/PR. The assigned dev >> wouldn't necessarily be responsible for review, but they would be >> responsible for chasing up other reviewers. >> >> - NEVER close a PR without the explicit consent of the contributor, OR after >> the contributor has been non-responsive for e.g. 1mo and two pings. In this >> last situation I would even suggest that we need two core devs to sign off. > > I would not close old PR, for the sake of closing them. If the > contributor is not interested in finishing the contribution and the > patch is almost ready, it might be a good way to introduce new > contributors (/students) to the PR. This can probably be done by an > "Need contributor" tag + "Easy fix", though I haven't thought more > about this > >> Other suggestions welcome in this thread. We should try to get a new process >> hammered out very soon. >> >> I also want to acknowledge @soupault for his triage/labelling work, which is >> a massive step in the right direction. But we need to follow up his triage >> with some actual process. >> >> Juan. >> >> -- >> 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+unsubscribe at googlegroups.com. >> To post to this group, send email to scikit-image at googlegroups.com. >> To view this discussion on the web, visit >> https://groups.google.com/d/msgid/scikit-image/CA%2BJHcKSh-k%2ByM0yBTRzTy%3DZgY7%2BOoEmPkKNA4xUgudeyhCJ5Dw%40mail.gmail.com. >> For more options, visit https://groups.google.com/d/optout. > > -- > 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+unsubscribe at googlegroups.com. > To post to this group, send an email to scikit-image at googlegroups.com. > To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/CAE-UAvSnKid2zn9bM4%3DdU2mvG96jDg8%2BfTayEOw%3DTA%2BS4u27zg%40mail.gmail.com. > For more options, visit https://groups.google.com/d/optout. -------------- next part -------------- An HTML attachment was scrubbed... URL: From leenagour at gmail.com Thu Sep 15 02:18:31 2016 From: leenagour at gmail.com (LC) Date: Wed, 14 Sep 2016 23:18:31 -0700 (PDT) Subject: how to find the intersection point of two objects Message-ID: <495f4f85-3d28-43fb-a157-18940600734c@googlegroups.com> Dear All, I am new to image processing and using OpenCV on python for implementing a part of research work. The aim is : - To identify the predecessor and successor of an object (shape) and - To calculate the Indegree(edges coming on shape) and outdegree(edges going out from shape) of object. Or is thr anyway to find digraph for given image? Can anybody help to find the intersection point of two object called rectangle and edges(directed line) in the attached img? your guidance /pointers will be appriciated. thanks & regards -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: input_img.jpg Type: image/jpeg Size: 22890 bytes Desc: not available URL: From jni.soma at gmail.com Thu Sep 15 09:29:20 2016 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Thu, 15 Sep 2016 06:29:20 -0700 Subject: Task board In-Reply-To: <1473894533.1455710.726083169.1D4C654B@webmail.messagingengine.com> References: <1472501868.510757.709588497.3AE0E834@webmail.messagingengine.com> <1473894533.1455710.726083169.1D4C654B@webmail.messagingengine.com> Message-ID: Yes, crazy timing! =D On 15 September 2016 at 9:08:59 AM, Stefan van der Walt ( stefanv at berkeley.edu) wrote: On Mon, Aug 29, 2016, at 13:17, Stefan van der Walt wrote: > I have some ideas around (1) that need fleshing out, but in the mean > time I was looking at http://zube.io to address part of (2). Take a look at this! https://github.com/blog/2256-a-whole-new-github-universe-announcing-new-tools-forums-and-features E.g., here's an empty project to play around with: https://github.com/scikit-image/scikit-image/projects/1 St?fan -- 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+unsubscribe at googlegroups.com. To post to this group, send an email to scikit-image at googlegroups.com. To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/1473894533.1455710.726083169.1D4C654B%40webmail.messagingengine.com. For more options, visit https://groups.google.com/d/optout. -------------- next part -------------- An HTML attachment was scrubbed... URL: From fboulogne at sciunto.org Fri Sep 16 04:35:48 2016 From: fboulogne at sciunto.org (=?UTF-8?Q?Fran=c3=a7ois_Boulogne?=) Date: Fri, 16 Sep 2016 10:35:48 +0200 Subject: Task board In-Reply-To: References: <1472501868.510757.709588497.3AE0E834@webmail.messagingengine.com> <1473894533.1455710.726083169.1D4C654B@webmail.messagingengine.com> Message-ID: <5d31ccd2-c6b7-903b-9d92-8a5095a92c6c@sciunto.org> I'm just discovering this new feature. It looks like we need to organize ourself because sorting issues in the column of a project is like duplicating the labels "status" we have on issues. I didn't find a way to automatically import issues, but we can search a label and drag the "cards". I think we need to determine how many boards we want (what github call project, I don't like this word... anyway). A big one with the progress or small ones, one per submodule? or one per core dev? Any thoughts? From l.roca at gmx.us Sat Sep 17 07:59:25 2016 From: l.roca at gmx.us (l.roca at gmx.us) Date: Sat, 17 Sep 2016 04:59:25 -0700 (PDT) Subject: Splits binary object to approximated ellipses using scikit-image Message-ID: <2097e7f7-9c21-4104-8aa4-8ad73b457cd3@googlegroups.com> Hi, Can scikit-image do ellipse splitting like in an imageJ plugin (http://imagej.net/Ellipse_split) that splits binary object to approximated ellipses? Thanks, Lluis -------------- next part -------------- An HTML attachment was scrubbed... URL: From ioannisgkan259 at gmail.com Sat Sep 17 14:57:15 2016 From: ioannisgkan259 at gmail.com (ioannisgkan259 at gmail.com) Date: Sat, 17 Sep 2016 11:57:15 -0700 (PDT) Subject: GLCM calculation using scikit-learn. Error when using greycomatrix Message-ID: <520f5f2b-4750-4b56-a40b-28b938b750d8@googlegroups.com> Hello everyone, I am using a SAR image (16-bit) and trying to implement GLCM algorithm using sciki-learn. When trying to calculate the GLCM using greycomatrix i get the following error: assert image.max() < levels. It says that the maximum value of the image intensity must be less than the number of grey levels. Because the SAR image is really big, i want to reduce the calculation time by reducing the levels to 8. Even if i remove the parameter 'level=8' when using greycomatrix, still gives me the same error My code is the following: from skimage.feature import greycomatrix, greycoprops import numpy as np from skimage import data import rasterio path = 'C:\Users\GLCM_implementation\glasgow.tif' with rasterio.open(path, 'r') as src: import_file = src.read() img = import_file[0,:,:] #i need only the two dimentions (height, width) print img.shape #calculate the GLCM specifying the distance, direction(4 directions) and number of grey levels GLCM = greycomatrix(img, [1], [0, np.pi/4, np.pi/2, 3*np.pi/4],levels=8, symmetric=False, normed=True) #list(GLCM[:,:,0,2]) #Calculate texture statistics contrast = greycoprops(GLCM, 'contrast') dissimilarity = greycoprops(GLCM, 'dissimilarity') homogeneity = greycoprops(GLCM, 'homogeneity') energy = greycoprops(GLCM, 'energy') correlation = greycoprops(GLCM, 'correlation') ASM = greycoprops(GLCM, 'ASM') Error message: 101 image = np.ascontiguousarray(image) 102 assert image.min() >= 0--> 103 assert image.max() < levels 104 image = image.astype(np.uint8) 105 distances = np.ascontiguousarray(distances, dtype=np.float64) AssertionError: I would appreciate any help. Thank you in advance Ioannis -------------- next part -------------- An HTML attachment was scrubbed... URL: From ioannisgkan259 at gmail.com Mon Sep 19 10:41:07 2016 From: ioannisgkan259 at gmail.com (ioannisgkan259 at gmail.com) Date: Mon, 19 Sep 2016 07:41:07 -0700 (PDT) Subject: GLCM calculation using scikit-learn. Error when using greycomatrix In-Reply-To: References: <520f5f2b-4750-4b56-a40b-28b938b750d8@googlegroups.com> Message-ID: <3c6b3c19-f3d8-49c6-9ffa-3942fc08ef55@googlegroups.com> Thank you very much Juan for your quick reply. That was helpful :) Ioannis On Monday, 19 September 2016 01:03:45 UTC+1, Juan Nunez-Iglesias wrote: > > Hi Ioannis, > > Unfortunately the levels keyword is used as a hint to the function about > the number of levels when the image is uint16, because the possible number > of levels is huge. But if you want to convert the image to those levels, > you have to do it manually. I suggest you look at the "rescale_intensity" > function: > > > http://scikit-image.org/docs/dev/api/skimage.exposure.html#skimage.exposure.rescale_intensity > > and process your image before passing it to the glcm function. > > I hope this helps! Keep pinging if you have more questions. =) > > Juan. > > On Sun, Sep 18, 2016 at 4:57 AM, > > wrote: > >> Hello everyone, >> >> I am using a SAR image (16-bit) and trying to implement GLCM algorithm >> using sciki-learn. When trying to calculate the GLCM using greycomatrix i >> get the following error: >> >> assert image.max() < levels. It says that the maximum value of the image intensity must be less than the number of grey levels. >> Because the SAR image is really big, i want to reduce the calculation time by reducing the levels to 8. >> Even if i remove the parameter 'level=8' when using greycomatrix, still gives me the same error >> >> My code is the following: >> >> from skimage.feature import greycomatrix, greycoprops >> import numpy as np >> from skimage import data >> import rasterio >> >> path = 'C:\Users\GLCM_implementation\glasgow.tif' >> >> with rasterio.open(path, 'r') as src: >> import_file = src.read() >> img = import_file[0,:,:] #i need only the two dimentions (height, width) >> print img.shape >> >> >> #calculate the GLCM specifying the distance, direction(4 directions) and number of grey levels >> GLCM = greycomatrix(img, [1], [0, np.pi/4, np.pi/2, 3*np.pi/4],levels=8, symmetric=False, normed=True) >> #list(GLCM[:,:,0,2]) >> >> >> #Calculate texture statistics >> contrast = greycoprops(GLCM, 'contrast') >> >> dissimilarity = greycoprops(GLCM, 'dissimilarity') >> >> homogeneity = greycoprops(GLCM, 'homogeneity') >> >> energy = greycoprops(GLCM, 'energy') >> >> correlation = greycoprops(GLCM, 'correlation') >> >> ASM = greycoprops(GLCM, 'ASM') >> >> >> >> Error message: >> >> 101 image = np.ascontiguousarray(image) 102 assert image.min() >= 0--> 103 assert image.max() < levels 104 image = image.astype(np.uint8) 105 distances = np.ascontiguousarray(distances, dtype=np.float64) >> AssertionError: >> >> >> I would appreciate any help. >> Thank you in advance >> >> Ioannis >> >> -- >> 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... at googlegroups.com . >> To post to this group, send email to scikit... at googlegroups.com >> . >> To view this discussion on the web, visit >> https://groups.google.com/d/msgid/scikit-image/520f5f2b-4750-4b56-a40b-28b938b750d8%40googlegroups.com >> >> . >> For more options, visit https://groups.google.com/d/optout. >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Sun Sep 18 20:03:23 2016 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Mon, 19 Sep 2016 10:03:23 +1000 Subject: GLCM calculation using scikit-learn. Error when using greycomatrix In-Reply-To: <520f5f2b-4750-4b56-a40b-28b938b750d8@googlegroups.com> References: <520f5f2b-4750-4b56-a40b-28b938b750d8@googlegroups.com> Message-ID: Hi Ioannis, Unfortunately the levels keyword is used as a hint to the function about the number of levels when the image is uint16, because the possible number of levels is huge. But if you want to convert the image to those levels, you have to do it manually. I suggest you look at the "rescale_intensity" function: http://scikit-image.org/docs/dev/api/skimage.exposure.html#skimage.exposure.rescale_intensity and process your image before passing it to the glcm function. I hope this helps! Keep pinging if you have more questions. =) Juan. On Sun, Sep 18, 2016 at 4:57 AM, wrote: > Hello everyone, > > I am using a SAR image (16-bit) and trying to implement GLCM algorithm > using sciki-learn. When trying to calculate the GLCM using greycomatrix i > get the following error: > > assert image.max() < levels. It says that the maximum value of the image intensity must be less than the number of grey levels. > Because the SAR image is really big, i want to reduce the calculation time by reducing the levels to 8. > Even if i remove the parameter 'level=8' when using greycomatrix, still gives me the same error > > My code is the following: > > from skimage.feature import greycomatrix, greycoprops > import numpy as np > from skimage import data > import rasterio > > path = 'C:\Users\GLCM_implementation\glasgow.tif' > > with rasterio.open(path, 'r') as src: > import_file = src.read() > img = import_file[0,:,:] #i need only the two dimentions (height, width) > print img.shape > > > #calculate the GLCM specifying the distance, direction(4 directions) and number of grey levels > GLCM = greycomatrix(img, [1], [0, np.pi/4, np.pi/2, 3*np.pi/4],levels=8, symmetric=False, normed=True) > #list(GLCM[:,:,0,2]) > > > #Calculate texture statistics > contrast = greycoprops(GLCM, 'contrast') > > dissimilarity = greycoprops(GLCM, 'dissimilarity') > > homogeneity = greycoprops(GLCM, 'homogeneity') > > energy = greycoprops(GLCM, 'energy') > > correlation = greycoprops(GLCM, 'correlation') > > ASM = greycoprops(GLCM, 'ASM') > > > > Error message: > > 101 image = np.ascontiguousarray(image) 102 assert image.min() >= 0--> 103 assert image.max() < levels 104 image = image.astype(np.uint8) 105 distances = np.ascontiguousarray(distances, dtype=np.float64) > AssertionError: > > > I would appreciate any help. > Thank you in advance > > Ioannis > > -- > 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+unsubscribe at googlegroups.com. > To post to this group, send email to scikit-image at googlegroups.com. > To view this discussion on the web, visit https://groups.google.com/d/ > msgid/scikit-image/520f5f2b-4750-4b56-a40b-28b938b750d8%40googlegroups.com > > . > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Sun Sep 18 20:09:20 2016 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Mon, 19 Sep 2016 10:09:20 +1000 Subject: Splits binary object to approximated ellipses using scikit-image In-Reply-To: <2097e7f7-9c21-4104-8aa4-8ad73b457cd3@googlegroups.com> References: <2097e7f7-9c21-4104-8aa4-8ad73b457cd3@googlegroups.com> Message-ID: Hi Lluis, We don't have a built-in function, but it should be relatively easy to build this using: scipy.ndimage.distance_transform: http://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.distance_transform_edt.html#scipy.ndimage.distance_transform_edt skimage.morphology.watershed: http://scikit-image.org/docs/dev/api/skimage.morphology.html#skimage.morphology.watershed skimage.transform.hough_circle: http://scikit-image.org/docs/dev/auto_examples/plot_circular_elliptical_hough_transform.html If you get it working, please post your results back to this list, as they would make a very nice example! Hope that helps, Juan. On Sat, Sep 17, 2016 at 9:59 PM, wrote: > Hi, > > > Can scikit-image do ellipse splitting like in an imageJ plugin ( > http://imagej.net/Ellipse_split) that splits binary object to > approximated ellipses? > > > Thanks, > > Lluis > > -- > 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+unsubscribe at googlegroups.com. > To post to this group, send email to scikit-image at googlegroups.com. > To view this discussion on the web, visit https://groups.google.com/d/ > msgid/scikit-image/2097e7f7-9c21-4104-8aa4-8ad73b457cd3%40googlegroups.com > > . > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Tue Sep 20 13:34:50 2016 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Tue, 20 Sep 2016 10:34:50 -0700 Subject: Task board In-Reply-To: <5d31ccd2-c6b7-903b-9d92-8a5095a92c6c@sciunto.org> References: <1472501868.510757.709588497.3AE0E834@webmail.messagingengine.com> <1473894533.1455710.726083169.1D4C654B@webmail.messagingengine.com> <5d31ccd2-c6b7-903b-9d92-8a5095a92c6c@sciunto.org> Message-ID: <1474392890.2276972.731679577.39AE1588@webmail.messagingengine.com> On Fri, Sep 16, 2016, at 01:35, Fran?ois Boulogne wrote: > I think we need to determine how many boards we want (what github call > project, I don't like this word... anyway). > A big one with the progress or small ones, one per submodule? or one per > core dev? I think each board is associated with an outcome. So, e.g., we will decide on some projects such as "Improve Documentation", or "Add 3D capability", or "Catch up on review backlog". Each of those will then have a few standard columns that we have to decide on. An initial suggestion would be: Inbox (list all relevant PRs) In Progress (someone is working on it) Ready for Review (please review this work) Done Would that cover 80% of use cases, or do we need more columns? St?fan From fboulogne at sciunto.org Tue Sep 20 14:17:04 2016 From: fboulogne at sciunto.org (=?UTF-8?Q?Fran=c3=a7ois_Boulogne?=) Date: Tue, 20 Sep 2016 20:17:04 +0200 Subject: Task board In-Reply-To: <1474392890.2276972.731679577.39AE1588@webmail.messagingengine.com> References: <1472501868.510757.709588497.3AE0E834@webmail.messagingengine.com> <1473894533.1455710.726083169.1D4C654B@webmail.messagingengine.com> <5d31ccd2-c6b7-903b-9d92-8a5095a92c6c@sciunto.org> <1474392890.2276972.731679577.39AE1588@webmail.messagingengine.com> Message-ID: <5edc406e-b7b9-c795-78b0-df1119557c60@sciunto.org> > I think each board is associated with an outcome. So, e.g., we will > decide on some projects such as "Improve Documentation", or "Add 3D > capability", or "Catch up on review backlog". Each of those will then > have a few standard columns that we have to decide on. OK with that. > An initial suggestion would be: > > Inbox (list all relevant PRs) > In Progress (someone is working on it) > Ready for Review (please review this work) > Done > > Would that cover 80% of use cases, or do we need more columns? Maybe we should had Needs Decision. Often, we have tickets stuck on a decision to take, either on new features (names, API...) or on refactoring (change API, dependencies, add new functions, reorganize a code...). These choices are often not straightforward and we need different opinions. -- Fran?ois Boulogne. http://www.sciunto.org GPG: 32D5F22F From jsch at demuc.de Tue Sep 20 15:56:39 2016 From: jsch at demuc.de (=?utf-8?Q?Johannes_Sch=C3=B6nberger?=) Date: Tue, 20 Sep 2016 21:56:39 +0200 Subject: Task board In-Reply-To: <1474392890.2276972.731679577.39AE1588@webmail.messagingengine.com> References: <1472501868.510757.709588497.3AE0E834@webmail.messagingengine.com> <1473894533.1455710.726083169.1D4C654B@webmail.messagingengine.com> <5d31ccd2-c6b7-903b-9d92-8a5095a92c6c@sciunto.org> <1474392890.2276972.731679577.39AE1588@webmail.messagingengine.com> Message-ID: <38EA86B6-C13E-4C8D-B6C9-AC74093C38A2@demuc.de> > On 20 Sep 2016, at 19:34, Stefan van der Walt wrote: > >> On Fri, Sep 16, 2016, at 01:35, Fran?ois Boulogne wrote: >> I think we need to determine how many boards we want (what github call >> project, I don't like this word... anyway). >> A big one with the progress or small ones, one per submodule? or one per >> core dev? > > I think each board is associated with an outcome. So, e.g., we will > decide on some projects such as "Improve Documentation", or "Add 3D > capability", or "Catch up on review backlog". Each of those will then > have a few standard columns that we have to decide on. > > An initial suggestion would be: > > Inbox (list all relevant PRs) > In Progress (someone is working on it) > Ready for Review (please review this work) > Done > > Would that cover 80% of use cases, or do we need more columns? This sounds good to me and we can add more columns as needed and as we gain some experience with the workflow. Grouping comments into reviews and then having a separate approval status is already a big step forward in my view. > > St?fan > > -- > 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+unsubscribe at googlegroups.com. > To post to this group, send an email to scikit-image at googlegroups.com. > To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/1474392890.2276972.731679577.39AE1588%40webmail.messagingengine.com. > For more options, visit https://groups.google.com/d/optout. -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Wed Sep 21 15:28:33 2016 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Wed, 21 Sep 2016 12:28:33 -0700 Subject: Dedicated work time from employers Message-ID: <1474486113.2732342.732994105.5DD428A0@webmail.messagingengine.com> Dear scikit-image developers In an effort to make it easier for you to contribute to scikit-image, I am sending letters to employers asking them to donate a certain amount of your work time (10 hours a month) to the project. If you are in a position where this would be helpful, please get in touch. The goal, ultimately, is to have have one (or preferably several) developers active daily in managing the project and reviewing code contributions. Best regards St?fan From silvertrumpet999 at gmail.com Wed Sep 21 19:32:30 2016 From: silvertrumpet999 at gmail.com (Josh Warner) Date: Wed, 21 Sep 2016 16:32:30 -0700 (PDT) Subject: Dedicated work time from employers In-Reply-To: <1474486113.2732342.732994105.5DD428A0@webmail.messagingengine.com> References: <1474486113.2732342.732994105.5DD428A0@webmail.messagingengine.com> Message-ID: Until June, my hands are tied. Surgery residency as an intern will do that. Right now, such a letter wouldn't really go very far. Starting after that point, I will be a Radiology resident. Infinitely superior hours, and my program director has offered 10-12 months of the following four years for research. I will be able to spend a sizeable chunk of that time being much more active. Wish I could do more in the short term, Josh On Wednesday, September 21, 2016 at 2:28:35 PM UTC-5, stefanv wrote: > > Dear scikit-image developers > > In an effort to make it easier for you to contribute to scikit-image, I > am sending letters to employers asking them to donate a certain amount > of your work time (10 hours a month) to the project. > > If you are in a position where this would be helpful, please get in > touch. > > The goal, ultimately, is to have have one (or preferably several) > developers active daily in managing the project and reviewing code > contributions. > > Best regards > St?fan > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Wed Sep 21 20:24:50 2016 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Wed, 21 Sep 2016 17:24:50 -0700 Subject: Dedicated work time from employers In-Reply-To: References: <1474486113.2732342.732994105.5DD428A0@webmail.messagingengine.com> Message-ID: <1474503890.2791614.733238033.1F77CA2F@webmail.messagingengine.com> Hi Josh On Wed, Sep 21, 2016, at 16:32, Josh Warner wrote: > Starting after that point, I will be a Radiology resident. Infinitely > superior hours, and my program director has offered 10-12 months of > the following four years for research. I will be able to spend a > sizeable chunk of that time being much more active. We look forward to having you back! Thanks for the feedback. St?fan -------------- next part -------------- An HTML attachment was scrubbed... URL: From dipugee at gmail.com Thu Sep 22 00:22:56 2016 From: dipugee at gmail.com (Dipankar Ganguly) Date: Wed, 21 Sep 2016 21:22:56 -0700 (PDT) Subject: skimage and opencv In-Reply-To: <20121228082507.GA27386@phare.normalesup.org> References: <1c1eacb6-349a-40c8-9058-faae9084e436@googlegroups.com> <20121228082507.GA27386@phare.normalesup.org> Message-ID: I have another question... If I use SciPy functions within Python 3.5 code how hard will be convert that code using JPython? On Friday, 28 December 2012 00:25:07 UTC-8, Emmanuelle Gouillart wrote: > > Hi Fran?ois, > > that's an excellent question, and not a troll :-). Opencv is a > very powerful library, but it focuses primarily on computer vision > (feature detection and extraction, classification, ...), as opposed to > image processing in general (with other tasks such as denoising, > segmentation, ...). > > The other big difference is that skimage builds on numpy > ndarrays, and uses the full power of the numpy API (including of course > the basic facilities for processing arrays as images that come with > numpy), as well as some of scipy functions (you could have added > scipy.ndimage to your list -- a few functions in skimage are wrappers > around scipy.ndimage, that exist for the sake of completeneness). One > important consequence is that algorithms working for 3-d or even n-d > images can be easily implemented in 3-d/n-d in skimage, whereas opencv is > restricted to 2-D images (as far as I know). Thanks to the use of numpy > arrays, the API of skimage is also quite pleasant for a numpy user, more > than the API of opencv. > > A related difference is that skimage is written in python and > cython, whereas opencv is a C++ library. The two libraries attract a > different crowd of developers, and a Python/Cython toolkit based on numpy > arrays is easier to develop and maintain inside the Scientific Python > ecosystem. > > I'm sure that other devs/users will have things to add to this > discussion! > > Cheers, > Emmanuelle > > On Thu, Dec 27, 2012 at 02:06:08PM -0800, Fran?ois wrote: > > Hi users and devs, > > > It came to my knowledge that another python library (based on C++ and > C > > codes) for image processing exists too : opencv > > I understand that numpy intregrates some basic features and we need > some > > advanced features but I have the feeling that skimages is redoundant > with > > opencv in some ways. > > What's the position of skimage about that? (Don't read this question > as a > > troll but like a real question). > > I mean that similar features exist in both. Would not be possible to > > reuse/integrate opencv or merge? what's the reason for keeping them > apart? > > > My observation is there is 4 libraries to manipulate images: > > * PIL > > * numpy > > * skimages > > * opencv > > That's a lot. > > > Cheers, > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dipugee at gmail.com Thu Sep 22 00:34:07 2016 From: dipugee at gmail.com (=?utf-8?B?RGlwYW5rYXIg4oCcRGlwdeKAnSBHYW5ndWx5?=) Date: Wed, 21 Sep 2016 21:34:07 -0700 Subject: Image edge detection In-Reply-To: References: <476b29f9-0e89-495d-aaee-88a9dbc69460@googlegroups.com> <5AB4F386-67B4-4DE3-9E2D-151F23C72F8C@gmail.com> <8FEA9192-98EE-4B8C-BC6E-7A1B6EFBFCE9@gmail.com> Message-ID: <5322EC72-2500-4022-B9EF-1E189F585B30@gmail.com> Hi Stefan: I need to bug you again. I have a couple of new questions? 1 My Python 3.5 code now includes Sci-Image, numpy and matplotlib functions as well some openCV calls. I need too convert this using JPython. How easily will these SciPy and openCV functions convert? 2. How close are SciImage and openCV in function content? Is there a document where I can find openCV equivalents to Sciimage functions and vice versa? Thanks. Dipu Dipankar Ganguly Consultant: Strategy/Technology/Commercialization Bothell, WA Cell: 408-203-8814 email: dipugee at gmail.com http://www.linkedin.com/in/dipugee > On Aug 9, 2016, at 2:42 PM, St?fan van der Walt wrote: > > Hi Dipu > > On 9 August 2016 at 14:40, Dipankar ?Dipu? Ganguly > wrote: > Sorry to bother you again. I am having trouble with "from skimage import xyz? commands. I am using Python 3.5 with Jupyter from Navigator. I am wondering if I am running into version mismatches. > > Yes, I am afraid we don't have an xyz submodule. > > Perhaps you can share some code with us, along with the error messages you are seeing? > > St?fan > > -- > 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/7IskXgM-99E/unsubscribe . > To unsubscribe from this group and all its topics, send an email to scikit-image+unsubscribe at googlegroups.com . > To post to this group, send email to scikit-image at googlegroups.com . > To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/CABDkGQnhpOQemWLzN5G2ACwwXgLca1cON1aCsmkBy283ZtHY2g%40mail.gmail.com . > For more options, visit https://groups.google.com/d/optout . -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Thu Sep 22 01:49:00 2016 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Wed, 21 Sep 2016 22:49:00 -0700 Subject: Image edge detection In-Reply-To: <5322EC72-2500-4022-B9EF-1E189F585B30@gmail.com> References: <476b29f9-0e89-495d-aaee-88a9dbc69460@googlegroups.com> <5AB4F386-67B4-4DE3-9E2D-151F23C72F8C@gmail.com> <8FEA9192-98EE-4B8C-BC6E-7A1B6EFBFCE9@gmail.com> <5322EC72-2500-4022-B9EF-1E189F585B30@gmail.com> Message-ID: Hi Dipu, 1. I assume you mean Jython. Most of the SciPy stack is not available for Jython, unless things have changed dramatically since I last looked at it? 2. I am not aware of a document translating between scikit-image and openCV. I suspect there is substantial non-overlap. Python bindings for both should operate on numpy arrays, so I think you should use both, wherever it makes sense? Though, as mentioned above, you will have more trouble with this using Jython? Juan. On 22 September 2016 at 2:34:12 pm, Dipankar ?Dipu? Ganguly ( dipugee at gmail.com) wrote: Hi Stefan: I need to bug you again. I have a couple of new questions? 1 My Python 3.5 code now includes Sci-Image, numpy and matplotlib functions as well some openCV calls. I need too convert this using JPython. How easily will these SciPy and openCV functions convert? 2. How close are SciImage and openCV in function content? Is there a document where I can find openCV equivalents to Sciimage functions and vice versa? Thanks. Dipu Dipankar Ganguly Consultant: Strategy/Technology/Commercialization Bothell, WA Cell: 408-203-8814 email: dipugee at gmail.com http://www.linkedin.com/in/dipugee On Aug 9, 2016, at 2:42 PM, St?fan van der Walt wrote: Hi Dipu On 9 August 2016 at 14:40, Dipankar ?Dipu? Ganguly wrote: > Sorry to bother you again. I am having trouble with "from skimage import > xyz? commands. I am using Python 3.5 with Jupyter from Navigator. I am > wondering if I am running into version mismatches. > Yes, I am afraid we don't have an xyz submodule. Perhaps you can share some code with us, along with the error messages you are seeing? St?fan -- 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/7IskXgM-99E/unsubscribe. To unsubscribe from this group and all its topics, send an email to scikit-image+unsubscribe at googlegroups.com. To post to this group, send email to scikit-image at googlegroups.com. To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/CABDkGQnhpOQemWLzN5G2ACwwXgLca1cON1aCsmkBy283ZtHY2g%40mail.gmail.com . For more options, visit https://groups.google.com/d/optout. -- 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+unsubscribe at googlegroups.com. To post to this group, send email to scikit-image at googlegroups.com. To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/5322EC72-2500-4022-B9EF-1E189F585B30%40gmail.com . For more options, visit https://groups.google.com/d/optout. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jsch at demuc.de Thu Sep 22 02:33:46 2016 From: jsch at demuc.de (=?utf-8?Q?Johannes_Sch=C3=B6nberger?=) Date: Thu, 22 Sep 2016 08:33:46 +0200 Subject: Dedicated work time from employers In-Reply-To: <1474486113.2732342.732994105.5DD428A0@webmail.messagingengine.com> References: <1474486113.2732342.732994105.5DD428A0@webmail.messagingengine.com> Message-ID: Hi Stefan, This is a great idea! Unfortunately, such an arrangement will not be possible on my side but I will try to help with reviews as much as time permits. I really hope someone has the option to take this great opportunity. Thanks for your efforts! Johannes > On Sep 21, 2016, at 9:28 PM, Stefan van der Walt wrote: > > Dear scikit-image developers > > In an effort to make it easier for you to contribute to scikit-image, I > am sending letters to employers asking them to donate a certain amount > of your work time (10 hours a month) to the project. > > If you are in a position where this would be helpful, please get in > touch. > > The goal, ultimately, is to have have one (or preferably several) > developers active daily in managing the project and reviewing code > contributions. > > Best regards > St?fan > > -- > 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+unsubscribe at googlegroups.com. > To post to this group, send an email to scikit-image at googlegroups.com. > To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/1474486113.2732342.732994105.5DD428A0%40webmail.messagingengine.com. > For more options, visit https://groups.google.com/d/optout. From dipugee at gmail.com Thu Sep 22 11:58:47 2016 From: dipugee at gmail.com (=?utf-8?B?RGlwYW5rYXIg4oCcRGlwdeKAnSBHYW5ndWx5?=) Date: Thu, 22 Sep 2016 08:58:47 -0700 Subject: Image edge detection In-Reply-To: References: <476b29f9-0e89-495d-aaee-88a9dbc69460@googlegroups.com> <5AB4F386-67B4-4DE3-9E2D-151F23C72F8C@gmail.com> <8FEA9192-98EE-4B8C-BC6E-7A1B6EFBFCE9@gmail.com> <5322EC72-2500-4022-B9EF-1E189F585B30@gmail.com> Message-ID: Thanks for the quick response Juan. Sorry. I DID mean Jython. The real issue is porting this hybrid Scikit-image/openCV/Python 3.5 code on to an Android tablet as an app. I am not an expert on that Android environment but thought Java was the common development platform. If there are other ways to accomplish that, I am all ears! Thanks. Dipu Dipankar ?Dipu? Ganguly dipugee at gmail.com Cell: 408-203-8814 > On Sep 21, 2016, at 10:49 PM, Juan Nunez-Iglesias wrote: > > Hi Dipu, > > 1. I assume you mean Jython. Most of the SciPy stack is not available for Jython, unless things have changed dramatically since I last looked at it? > > 2. I am not aware of a document translating between scikit-image and openCV. I suspect there is substantial non-overlap. Python bindings for both should operate on numpy arrays, so I think you should use both, wherever it makes sense? Though, as mentioned above, you will have more trouble with this using Jython? > > Juan. > > On 22 September 2016 at 2:34:12 pm, Dipankar ?Dipu? Ganguly (dipugee at gmail.com ) wrote: > >> Hi Stefan: >> >> I need to bug you again. I have a couple of new questions? >> >> 1 My Python 3.5 code now includes Sci-Image, numpy and matplotlib functions as well some openCV calls. I need too convert this using JPython. How easily will these SciPy and openCV functions convert? >> >> 2. How close are SciImage and openCV in function content? Is there a document where I can find openCV equivalents to Sciimage functions and vice versa? >> >> Thanks. >> >> Dipu >> >> >> Dipankar Ganguly >> Consultant: Strategy/Technology/Commercialization >> Bothell, WA >> Cell: 408-203-8814 >> email: dipugee at gmail.com >> http://www.linkedin.com/in/dipugee >> >> >> >> >> >> >> >> >> >>> On Aug 9, 2016, at 2:42 PM, St?fan van der Walt > wrote: >>> >>> Hi Dipu >>> >>> On 9 August 2016 at 14:40, Dipankar ?Dipu? Ganguly > wrote: >>> Sorry to bother you again. I am having trouble with "from skimage import xyz? commands. I am using Python 3.5 with Jupyter from Navigator. I am wondering if I am running into version mismatches. >>> >>> Yes, I am afraid we don't have an xyz submodule. >>> >>> Perhaps you can share some code with us, along with the error messages you are seeing? >>> >>> St?fan >>> >>> -- >>> 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/7IskXgM-99E/unsubscribe . >>> To unsubscribe from this group and all its topics, send an email to scikit-image+unsubscribe at googlegroups.com . >>> To post to this group, send email to scikit-image at googlegroups.com . >>> To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/CABDkGQnhpOQemWLzN5G2ACwwXgLca1cON1aCsmkBy283ZtHY2g%40mail.gmail.com . >>> For more options, visit https://groups.google.com/d/optout . >> >> -- >> 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+unsubscribe at googlegroups.com . >> To post to this group, send email to scikit-image at googlegroups.com . >> To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/5322EC72-2500-4022-B9EF-1E189F585B30%40gmail.com . >> For more options, visit https://groups.google.com/d/optout . > > -- > 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/7IskXgM-99E/unsubscribe . > To unsubscribe from this group and all its topics, send an email to scikit-image+unsubscribe at googlegroups.com . > To post to this group, send email to scikit-image at googlegroups.com . > To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/CA%2BJHcKR7UN8QVgN7btj8OyHJT_u%3DKQAkkqWPo1C9Lf5s9y3MYg%40mail.gmail.com . > For more options, visit https://groups.google.com/d/optout . -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Thu Sep 22 20:24:56 2016 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Thu, 22 Sep 2016 17:24:56 -0700 Subject: Dedicated work time from employers In-Reply-To: <20160922181734.GD446144@phare.normalesup.org> References: <1474486113.2732342.732994105.5DD428A0@webmail.messagingengine.com> <20160922181734.GD446144@phare.normalesup.org> Message-ID: Emma, you should try reading him St?fan's letter as a lullaby, maybe it will calm him down and it'll give you more time to work on scikit-image! =P On 23 September 2016 at 4:17:38 am, Emmanuelle Gouillart ( emmanuelle.gouillart at nsup.org) wrote: Dear St?fan, thanks for the initiative! My "employer" until December is a 2-week old little boy, and I hope that I'll soon be able to set aside a few hours every week for scikit-image, which will be a welcome change from lullabies and nappies :-). As for my regular employer, I'm afraid that my current position as group leader is not compatible with work on scikit-image during work hours, so I'll try to keep on contributing a little during evenings and week-ends. Best, Emma On Wed, Sep 21, 2016 at 12:28:33PM -0700, Stefan van der Walt wrote: > Dear scikit-image developers > In an effort to make it easier for you to contribute to scikit-image, I > am sending letters to employers asking them to donate a certain amount > of your work time (10 hours a month) to the project. > If you are in a position where this would be helpful, please get in > touch. > The goal, ultimately, is to have have one (or preferably several) > developers active daily in managing the project and reviewing code > contributions. > Best regards > St?fan -- 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+unsubscribe at googlegroups.com. To post to this group, send an email to scikit-image at googlegroups.com. To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/20160922181734.GD446144%40phare.normalesup.org. For more options, visit https://groups.google.com/d/optout. -------------- next part -------------- An HTML attachment was scrubbed... URL: From google at terre-adelie.org Thu Sep 22 12:26:51 2016 From: google at terre-adelie.org (=?UTF-8?B?SsOpcsO0bWU=?= Kieffer) Date: Thu, 22 Sep 2016 18:26:51 +0200 Subject: skimage and opencv In-Reply-To: References: <1c1eacb6-349a-40c8-9058-faae9084e436@googlegroups.com> <20121228082507.GA27386@phare.normalesup.org> Message-ID: <20160922182651.67add8f6@patagonia> On Wed, 21 Sep 2016 21:22:56 -0700 (PDT) Dipankar Ganguly wrote: > I have another question... > If I use SciPy functions within Python 3.5 code how hard will be convert > that code using JPython? hard ... ...as hard as calling fortran code from java From emmanuelle.gouillart at nsup.org Thu Sep 22 14:17:35 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Thu, 22 Sep 2016 20:17:35 +0200 Subject: Dedicated work time from employers In-Reply-To: <1474486113.2732342.732994105.5DD428A0@webmail.messagingengine.com> References: <1474486113.2732342.732994105.5DD428A0@webmail.messagingengine.com> Message-ID: <20160922181734.GD446144@phare.normalesup.org> Dear St??fan, thanks for the initiative! My "employer" until December is a 2-week old little boy, and I hope that I'll soon be able to set aside a few hours every week for scikit-image, which will be a welcome change from lullabies and nappies :-). As for my regular employer, I'm afraid that my current position as group leader is not compatible with work on scikit-image during work hours, so I'll try to keep on contributing a little during evenings and week-ends. Best, Emma On Wed, Sep 21, 2016 at 12:28:33PM -0700, Stefan van der Walt wrote: > Dear scikit-image developers > In an effort to make it easier for you to contribute to scikit-image, I > am sending letters to employers asking them to donate a certain amount > of your work time (10 hours a month) to the project. > If you are in a position where this would be helpful, please get in > touch. > The goal, ultimately, is to have have one (or preferably several) > developers active daily in managing the project and reviewing code > contributions. > Best regards > St??fan From jni.soma at gmail.com Fri Sep 23 02:17:56 2016 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Thu, 22 Sep 2016 23:17:56 -0700 Subject: Implementing Kadir and Brady's saliency detector in skimage? In-Reply-To: References: <7132cb6e-e66f-45be-a71a-327a2e5ff7d9@googlegroups.com> Message-ID: Hi Parul, Sorry for the silence! Sometimes we are busy and these PRs fall through the cracks. I'm doing a quick review of your code right now but I don't see any questions regarding parameters on the issue itself? For the gallery example, whatever code you used to apply the method to `data.astronaut` is probably a good choice for the example! Juan. From: Parul Sethi Reply: scikit-image at googlegroups.com Date: 23 September 2016 at 3:54:43 PM To: scikit-image at googlegroups.com Subject: Re: Implementing Kadir and Brady's saliency detector in skimage? Hi, I opened a PR regarding this Saliency detection algorithm few days back (#2299). Though the implementation is complete, i required some suggestions regarding parameters(mentioned there). Can any scikit-image maintainer please review it once. Thanks On Thu, Jul 28, 2016 at 11:33 AM, Parul Sethi wrote: > So sorry for the long pause. > > Thankyou for the response! > I'll soon be done with it. > On 11 Jul 2016 4:11 am, "St?fan van der Walt" > wrote: > >> Hi Parul >> >> We are happy to evaluate any PR for inclusion. Saliency detection is >> within scope. >> >> Best regards >> St?fan >> On Jul 6, 2016 05:54, "parul sethi" wrote: >> >>> Hi, >>> >>> I required to use Kadir and Brady's saliency detector for feature >>> extraction process, and didn't found it's python implementation. So, i was >>> in process of implementing the same. >>> Will it be of interest to skimage too? I can use some advice from >>> skimage maintainers to build it with specific suitability for skimage >>> module. >>> >>> Thank you. >>> -- >>> 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+unsubscribe at googlegroups.com. >>> To post to this group, send email to scikit-image at googlegroups.com. >>> To view this discussion on the web, visit https://groups.google.com/d/ >>> msgid/scikit-image/7132cb6e-e66f-45be-a71a-327a2e5ff7d9% >>> 40googlegroups.com >>> >>> . >>> For more options, visit https://groups.google.com/d/optout. >>> >> -- >> 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/FzZ1VkJt-Ks/unsubscribe. >> To unsubscribe from this group and all its topics, send an email to >> scikit-image+unsubscribe at googlegroups.com. >> To post to this group, send email to scikit-image at googlegroups.com. >> To view this discussion on the web, visit https://groups.google.com/d/ >> msgid/scikit-image/CABDkGQ%3D%2BcAy%3DLzc5MOR-CzummOuWiyDWrvoN_mXNX% >> 2BNBh868Ew%40mail.gmail.com >> >> . >> For more options, visit https://groups.google.com/d/optout. >> > -- Parul Sethi (student) B.Tech (IT & Mathematical innovation) Cluster Innovation Centre Delhi University -- 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+unsubscribe at googlegroups.com. To post to this group, send email to scikit-image at googlegroups.com. To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/CAFgV4O5DumqYxW-a0zm5vU9bd459TUpX2Ov9OhLbMNSc%3D%3DxgKg%40mail.gmail.com . For more options, visit https://groups.google.com/d/optout. -------------- next part -------------- An HTML attachment was scrubbed... URL: From parul1sethi at gmail.com Fri Sep 23 01:54:42 2016 From: parul1sethi at gmail.com (Parul Sethi) Date: Fri, 23 Sep 2016 11:24:42 +0530 Subject: Implementing Kadir and Brady's saliency detector in skimage? In-Reply-To: References: <7132cb6e-e66f-45be-a71a-327a2e5ff7d9@googlegroups.com> Message-ID: Hi, I opened a PR regarding this Saliency detection algorithm few days back (#2299). Though the implementation is complete, i required some suggestions regarding parameters(mentioned there). Can any scikit-image maintainer please review it once. Thanks On Thu, Jul 28, 2016 at 11:33 AM, Parul Sethi wrote: > So sorry for the long pause. > > Thankyou for the response! > I'll soon be done with it. > On 11 Jul 2016 4:11 am, "St?fan van der Walt" > wrote: > >> Hi Parul >> >> We are happy to evaluate any PR for inclusion. Saliency detection is >> within scope. >> >> Best regards >> St?fan >> On Jul 6, 2016 05:54, "parul sethi" wrote: >> >>> Hi, >>> >>> I required to use Kadir and Brady's saliency detector for feature >>> extraction process, and didn't found it's python implementation. So, i was >>> in process of implementing the same. >>> Will it be of interest to skimage too? I can use some advice from >>> skimage maintainers to build it with specific suitability for skimage >>> module. >>> >>> Thank you. >>> >>> -- >>> 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+unsubscribe at googlegroups.com. >>> To post to this group, send email to scikit-image at googlegroups.com. >>> To view this discussion on the web, visit https://groups.google.com/d/ >>> msgid/scikit-image/7132cb6e-e66f-45be-a71a-327a2e5ff7d9% >>> 40googlegroups.com >>> >>> . >>> For more options, visit https://groups.google.com/d/optout. >>> >> -- >> 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/FzZ1VkJt-Ks/unsubscribe. >> To unsubscribe from this group and all its topics, send an email to >> scikit-image+unsubscribe at googlegroups.com. >> To post to this group, send email to scikit-image at googlegroups.com. >> To view this discussion on the web, visit https://groups.google.com/d/ >> msgid/scikit-image/CABDkGQ%3D%2BcAy%3DLzc5MOR-CzummOuWiyDWrvoN_mXNX% >> 2BNBh868Ew%40mail.gmail.com >> >> . >> For more options, visit https://groups.google.com/d/optout. >> > -- Parul Sethi (student) B.Tech (IT & Mathematical innovation) Cluster Innovation Centre Delhi University -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeanpatrick.pommier at gmail.com Tue Sep 27 06:27:07 2016 From: jeanpatrick.pommier at gmail.com (Jean-Patrick Pommier) Date: Tue, 27 Sep 2016 03:27:07 -0700 (PDT) Subject: Generating a dataset of images in RAM Message-ID: Dear all, I proposed on kagle an image processing/supervised classification problem concerning the resolution of overlapping chromosomes.The aim is to produce a large dataset of examples. A first dataset was produced , but it seems to be too small to yield good results for supervised classification with a neural network. As explained in the first notebook, 8Go is not enough to process, mainly to resize/crop, the images. My question how a large batch of images >>100 000 can be resized? Thanks. Jean-Patrick PS I can't hide that It would be great if some would be interrested by the problem itself and give some help on the resolution itself or some advices on the proposed code. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Tue Sep 27 19:55:07 2016 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Tue, 27 Sep 2016 16:55:07 -0700 Subject: Generating a dataset of images in RAM In-Reply-To: References: Message-ID: Hi Jean-Patrick, Why do you need to load everything into RAM to resize it? This a perfect use-case for streaming data processing. Have a look at my notebook from EuroSciPy 2015 for some examples: https://github.com/jni/streaming-talk/blob/master/Big%20data%20in%20little%20laptop.ipynb Specifically, as you generate examples, you should be writing them to disk directly. Then you are limited by disk size, instead of RAM size. I hope that helps! Juan. On 27 September 2016 at 8:27:09 pm, Jean-Patrick Pommier ( jeanpatrick.pommier at gmail.com) wrote: Dear all, I proposed on kagle an image processing/supervised classification problem concerning the resolution of overlapping chromosomes.The aim is to produce a large dataset of examples. A first dataset was produced , but it seems to be too small to yield good results for supervised classification with a neural network. As explained in the first notebook, 8Go is not enough to process, mainly to resize/crop, the images. My question how a large batch of images >>100 000 can be resized? Thanks. Jean-Patrick PS I can't hide that It would be great if some would be interrested by the problem itself and give some help on the resolution itself or some advices on the proposed code. -- 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+unsubscribe at googlegroups.com. To post to this group, send email to scikit-image at googlegroups.com. To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/cc5cdf4e-6847-4872-a10f-a598148edf56%40googlegroups.com . For more options, visit https://groups.google.com/d/optout. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeanpatrick.pommier at gmail.com Wed Sep 28 01:17:27 2016 From: jeanpatrick.pommier at gmail.com (Jean-Patrick Pommier) Date: Tue, 27 Sep 2016 22:17:27 -0700 (PDT) Subject: Generating a dataset of images in RAM In-Reply-To: References: Message-ID: Thanks Juan, I didn't know toolz. Le mardi 27 septembre 2016 12:27:08 UTC+2, Jean-Patrick Pommier a ?crit : > > Dear all, > > I proposed on kagle an image processing/supervised classification problem > > concerning the resolution of overlapping chromosomes.The aim is to produce > a large dataset of examples. A first dataset was produced > , but it seems to > be too small to yield good results for supervised classification with a > neural network. As explained in the first notebook, 8Go is not enough to > process, mainly to resize/crop, the images. > My question how a large batch of images >>100 000 can be resized? > > Thanks. > > Jean-Patrick > > PS > I can't hide that It would be great if some would be interrested by the > problem itself and give some help on the resolution itself or some advices > on the proposed code. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pkmkicha at gmail.com Thu Sep 29 06:30:34 2016 From: pkmkicha at gmail.com (KRISHNAMOOORTHY P) Date: Thu, 29 Sep 2016 03:30:34 -0700 (PDT) Subject: Line Detection Message-ID: <05077510-f712-483b-a881-590bdff9f5e1@googlegroups.com> How to get oblique (+45 and 135 degree) of images using scikit-image or with any other packages? -------------- next part -------------- An HTML attachment was scrubbed... URL: From siqueiraaf at gmail.com Thu Sep 29 13:43:12 2016 From: siqueiraaf at gmail.com (Alexandre Fioravante de Siqueira) Date: Thu, 29 Sep 2016 10:43:12 -0700 (PDT) Subject: Fwd: PyData Community Cookbook - August Update In-Reply-To: References: <1472501613.509939.709586801.1704EAF6@webmail.messagingengine.com> <20160829204435.GC1302378@phare.normalesup.org> <1472576802.757608.710583985.061974DE@webmail.messagingengine.com> <20160830192254.GA1722536@phare.normalesup.org> <1472680444.2684150.712061369.2AC87F0C@webmail.messagingengine.com> <20160901170037.GB3064887@phare.normalesup.org> Message-ID: <5e3dbf6d-c3a7-47e0-9a52-9ab184631015@googlegroups.com> Hi all, did you lose interest on working on this project? If you don't want to work on that anymore, please tell me. I think I can't work on that alone, and I would need to stop this project. Thanks, Alex Em quarta-feira, 14 de setembro de 2016 15:20:40 UTC+2, Alexandre Fioravante de Siqueira escreveu: > > Hi all, > like Emmanuelle said in this previous e-mail, it's time to think about the > content. > Would you like to point any gallery examples for that? What do you think > it's important to be in that chapter? > I was thinking on a first section about the basics: open a file, separate > the color channels, present histograms, all that stuff. > Thanks. Looking forward to work with you, > > Alex > > Em quinta-feira, 1 de setembro de 2016 19:00:40 UTC+2, Emmanuelle > Gouillart escreveu: >> >> ... it's a good time to start thinking about the content. Even if it's >> advertised as a "cookbook", I think that a length of 15-20 pages is >> enough to present both "recipes" and also some big picture stuff (why and >> when use scikit-image or other image processing libraries? what are the >> typical coding patterns? etc.). As for the recipes, if we can re-use some >> of our gallery examples it will save us some precious time. How about we >> select one example if each of the chapters of the gallery and we take >> advantage of the cookbook to improve it? >> >> Best, >> Emma >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From emmanuelle.gouillart at nsup.org Fri Sep 30 13:41:55 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Fri, 30 Sep 2016 19:41:55 +0200 Subject: Fwd: PyData Community Cookbook - August Update In-Reply-To: <5e3dbf6d-c3a7-47e0-9a52-9ab184631015@googlegroups.com> References: <20160829204435.GC1302378@phare.normalesup.org> <1472576802.757608.710583985.061974DE@webmail.messagingengine.com> <20160830192254.GA1722536@phare.normalesup.org> <1472680444.2684150.712061369.2AC87F0C@webmail.messagingengine.com> <20160901170037.GB3064887@phare.normalesup.org> <5e3dbf6d-c3a7-47e0-9a52-9ab184631015@googlegroups.com> Message-ID: <20160930174155.GC1950009@phare.normalesup.org> Hi Alex, don't worry, it's just that it's harder to find motivation when the deadline is not that close ;-). But of course we should get started. How about you propose an outline with different sections (a first one with the basics as you suggest, then different image processing tasks, ...) and ask for volunteers for the different sections? I could take care of segmentation for example. Best, Emma On Thu, Sep 29, 2016 at 10:43:12AM -0700, Alexandre Fioravante de Siqueira wrote: > Hi all, > did you lose interest on working on this project? > If you don't want to work on that anymore, please tell me. I think I can't work > on that alone, and I would need to stop this project. > Thanks, > Alex > Em quarta-feira, 14 de setembro de 2016 15:20:40 UTC+2, Alexandre Fioravante de > Siqueira escreveu: > Hi all, > like Emmanuelle said in this previous e-mail, it's time to think about the > content. > Would you like to point any gallery examples for that? What do you think > it's important to be in that chapter? > I was thinking on a first section about the basics: open a file, separate > the color channels, present histograms, all that stuff. > Thanks. Looking forward to work with you, > Alex?? > Em quinta-feira, 1 de setembro de 2016 19:00:40 UTC+2, Emmanuelle Gouillart > escreveu: > ... it's a good time to start thinking about the content. Even if it's > advertised as a "cookbook", I think that a length of 15-20 pages is > enough to present both "recipes" and also some big picture stuff (why > and > when use scikit-image or other image processing libraries? what are the > typical coding patterns? etc.). As for the recipes, if we can re-use > some > of our gallery examples it will save us some precious time. How about > we > select one example if each of the chapters of the gallery and we take > advantage of the cookbook to improve it? > Best, > Emma