Mailman 3 August 2011 - scikit-image

Re: Progress towards the next release
by Chris Colbert Aug. 30, 2011

Aug. 30, 2011

What? It is was a clean patch :) On Aug 30, 2011 6:36 AM, "Stéfan van der Walt" <stefan(a)sun.ac.za> wrote: > Hi all, > > We've made some progress at the sprint last night towards the 0.3 > release. Thanks go out to Emmanuelle, Gaël, Thouis, David as well as > Chris (whom we never saw, but who merged a patch silently :). > > I'll be travelling for the next 10 days, but thereafter I plan to > round this up and cut the release. Here's what's cooking: > > - Emmanuelle is incorporating cellprofiler morphology funcs (watershed & others) > - Stefan is creating the Debian packages, sorting out the windows > builder, and writing up the dtype overview > - Thouis & Kyle are completing the functionality overview table > - Gael is improving the implementation of TV denoise using fista > - David is setting up our bento build script > - The team (that's you!) is reviewing Pieter's Google Summer of Code patches > > We need to hear from you! If there's anything you need to get in > before the release, now's a good time. > > Also, we need a new logo for the website--I know someone must be able > to draw prettier pictures than me, so don't be shy! > > http://github.com/scikits-image > > Regards > Stéfan

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Progress towards the next release
by Stéfan van der Walt Aug. 30, 2011

Aug. 30, 2011

Hi all, We've made some progress at the sprint last night towards the 0.3 release. Thanks go out to Emmanuelle, Gaël, Thouis, David as well as Chris (whom we never saw, but who merged a patch silently :). I'll be travelling for the next 10 days, but thereafter I plan to round this up and cut the release. Here's what's cooking: - Emmanuelle is incorporating cellprofiler morphology funcs (watershed & others) - Stefan is creating the Debian packages, sorting out the windows builder, and writing up the dtype overview - Thouis & Kyle are completing the functionality overview table - Gael is improving the implementation of TV denoise using fista - David is setting up our bento build script - The team (that's you!) is reviewing Pieter's Google Summer of Code patches We need to hear from you! If there's anything you need to get in before the release, now's a good time. Also, we need a new logo for the website--I know someone must be able to draw prettier pictures than me, so don't be shy! http://github.com/scikits-image Regards Stéfan

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Re: Removing OpenCV wrappers
by Pieter Holtzhausen Aug. 29, 2011

Aug. 29, 2011

Our version can prove as example of how it should have been done :) but yes the opencv wrapper now offers the same functionality while being more thorough and more actively maintained. 2011/8/29 Stéfan van der Walt <stefan(a)sun.ac.za>: > Hi all, > > The OpenCV wrappers currently in scikits.image did a great job, but > since the OpenCV project's wrappers have now caught up (in terms of > not copying data, etc.), it makes sense to deprecate ours for removal > in the next release. > > Please let me know if you have any thoughts on the topic. > > Regards > Stéfan >

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Removing OpenCV wrappers
by Stéfan van der Walt Aug. 29, 2011

Aug. 29, 2011

Hi all, The OpenCV wrappers currently in scikits.image did a great job, but since the OpenCV project's wrappers have now caught up (in terms of not copying data, etc.), it makes sense to deprecate ours for removal in the next release. Please let me know if you have any thoughts on the topic. Regards Stéfan

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Re: Usage of and relationship to OpenCV
by Thouis (Ray) Jones Aug. 29, 2011

Aug. 29, 2011

2011/8/29 Stéfan van der Walt <stefan(a)sun.ac.za>: > Should we declare OpenCV a dependency? If it's made a dependency, is it possible to automate the process of fetching and installing it (in a directory local to the package?) as part of the install process? Only if it's not installed already, of course. I think I would prefer: - not making it a dependency - adding code to (optionally) download and install it as part of the scikit install process - some functionality might require it be installed. Eventually, slower non-opencv versions might be added. Ray

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Re: Usage of and relationship to OpenCV
by Emmanuelle Gouillart Aug. 29, 2011

Aug. 29, 2011

Hi, having opencv as a dependency has two important drawbacks for me. First, it makes the installation of the scikit more difficult. Second, the documentation of openCV does not match the standards of numpy/scipy docstrings (no examples, few references to articles). Performance is great, but I think we'll gain more users by putting effort on user-friendliness than if we put it on performance. For examples, a large fraction of my colleagues are using image processing, but on Windows, and they get discouraged by a package with unsufficient documentation. I'm at the Python for Physics day now and I don't have the time to write more, but I'll be glad to continue the discussion later. Cheers, Emmanuelle On Mon, Aug 29, 2011 at 11:25:06AM +0200, StÃ¯Â¿Â½fan van der Walt wrote: > Hi all, > After merging the GSoC contributions, I think we're in good shape for > a next release. Before we get there, however, I'd like to ask your > opinions. > Should we declare OpenCV a dependency? There are two sides to this: > 1) I want to stop focusing on optimising low-level routines, and > instead implement interesting algorithms but 2) OpenCV is quite a big > dependency (although it does run on Windows, Linux, Mac etc, comes > with built binaries in all of them, and has a permissive BSD license). > Fact is, our manpower is limited, so we should focus on where we can > make a difference. My aim is to provide an excellent image processing > toolbox for Python that at least covers the MATLAB functionality and > more, and to reach that goal with our limited manpower, we need to > carefully pick our strategy. > I'd be glad to hear what you have to say. > Regards > StÃ¯Â¿Â½fan

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Report from EuroSciPy
by Stéfan van der Walt Aug. 29, 2011

Aug. 29, 2011

Hi everyone, A quick report from EuroSciPy: - Ray Jones gave a great talk about CellProfiler. As you may recall, CellProfiler opened their code under a BSD license so that we may include it in the scikit. - There will be a sprint this evening at 19:30 Paris time to move us closer to our 0.3 release. Emmanuelle, Ray and myself will be sprinting from Paris, and you are all invited to join via IRC or chat. - We've had good conversations with developers of other image processing packages, so let's hope for some more contributors! Stéfan

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Usage of and relationship to OpenCV
by Stéfan van der Walt Aug. 29, 2011

Aug. 29, 2011

Hi all, After merging the GSoC contributions, I think we're in good shape for a next release. Before we get there, however, I'd like to ask your opinions. Should we declare OpenCV a dependency? There are two sides to this: 1) I want to stop focusing on optimising low-level routines, and instead implement interesting algorithms but 2) OpenCV is quite a big dependency (although it does run on Windows, Linux, Mac etc, comes with built binaries in all of them, and has a permissive BSD license). Fact is, our manpower is limited, so we should focus on where we can make a difference. My aim is to provide an excellent image processing toolbox for Python that at least covers the MATLAB functionality and more, and to reach that goal with our limited manpower, we need to carefully pick our strategy. I'd be glad to hear what you have to say. Regards Stéfan

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Re: Greyscale reconstruction and merging CellProfiler code
by Stéfan van der Walt Aug. 21, 2011

Aug. 21, 2011

On Sun, Aug 21, 2011 at 7:21 AM, Tony Yu <tsyu80(a)gmail.com> wrote: > It sounds like there are plans to decide on a tutorial format at EuroScipy, > so I'm inclined to wait until the dust has settled. Also, do you think the > morphological reconstruction routine looks general/useful enough to include? I'll have to study the technique in a bit more detail. I'd like to compare it with the Discrete Pulse Transform, for example: http://dip.sun.ac.za/~stefan/dpt/ http://scholar.sun.ac.za/handle/10019.1/4883 Regards Stéfan

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Re: scikits.image sprints at EuroScipy and SciPy 2011
by Emmanuelle Gouillart Aug. 21, 2011

Aug. 21, 2011

Hi StÃ¯Â¿Â½fan! > I'll definitely be there. I think one of the main aims of the sprint > for me will be to Great news! When do you arrive in Paris? > - Merge and test Pieter Holtzhausen's GSoC changes > - Add tools for easy writing of tutorials (we'll borrow from nipy, perhaps) > - Fill out the MATLAB compatibility chart that Kyle Mandli > implemented at SciPy2011 > - Prepare for the release of 0.3 OK, I'll try to give you a hand for this. As for me, I'm particularly interested in writing documentation (examples) and merging code from CellProfiler. > > Let's start: I'm free on Tuesday 23rd and Wednesday 24th; I'll have much > > less time during the conference itself, being one of the organizers. > I'll definitely be there those days as well. I'm teaching during the > conference, but apart from that I'll work on this and IPython. Great; in fact I'll have to be at work either on Tuesday morning or Wednesday morning, but I'll be at the Ecole Normale SupÃ¯Â¿Â½rieure (Physics Department) for the rest of the time. Anybody else? (MaÃ¯Â¿Â½l?)

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