Mailman 3 April 2016 - scikit-image

Re: release: scikit-image 0.12 is out!
by Emmanuelle Gouillart 28 Apr '16

28 Apr '16

not yet I'm afraid :-) pip install will get you the latest version, so it should be 0.12.3 On Wed, Apr 27, 2016 at 11:51:16PM -0700, Raphael Okoye wrote: > hi Emmanuelle, > Â hehehe...hope u have your coffee now..Thanks for the reply. So pip install > --upgrade scikit-image will land me in which version? 0.12.0? On the > announcements on the website http://scikit-image.org/ it seems that's the > latest stable version (although the right top corner of the page says 0.12.3 is > the latest) . > On 27 April 2016 at 23:45, Emmanuelle Gouillart <emmanuelle.gouillart(a)nsup.org> > wrote: > Sorry, I meant for 0.12. Morning answers before coffee are not reliable > :-) > On Thu, Apr 28, 2016 at 08:43:44AM +0200, Emmanuelle Gouillart wrote: > > Hi Raphael, > > I don't think we have an Ubuntu package yet for 0.11. The way to go would > > be to use pip, with "pip install --upgrade scikit-image". > > Cheers, > > Emma > > On Wed, Apr 27, 2016 at 04:59:41PM -0700, Raphael Okoye wrote: > > > hi Emmanuel, > > > Â > > > Â I need help with installation of Â the latest version of scikit image > (the > > > version I have is 0.11.3 kindly find attached). I currently run Ubuntu > 14.04 > > > LTS and running python 3.4.3. I'm not sure ifÂ Â Â sudo apt-get build-dep > python- > > > scikit-image Â Â Â is the way to go or ifÂ > > > pip install --upgrade scikit-image do the necessary upgrade for me.Â Â > Any > > > guidance will be highly appreciated.Â > > > Thank you. > > > On Monday, 7 March 2016 13:50:11 UTC-8, Emmanuelle Gouillart wrote: > > >Â Â Â Announcement: scikit-image 0.12 > > >Â Â Â =============================== > > >Â Â Â The scikit-image team is very pleased to announce the release of > version > > >Â Â Â 0.12 of scikit-image. > > >Â Â Â scikit-image is an image processing toolbox for Python and SciPy, > that > > >Â Â Â includes algorithms for segmentation, geometric transformations, > color > > >Â Â Â space manipulation, analysis, filtering, morphology, feature > detection, > > >Â Â Â and more, for 2-D and 3-D (sometimes n-D) images. > > >Â Â Â For more information, examples, and documentation, please visit our > > >Â Â Â website: > > >Â Â Â http://scikit-image.org > > >Â Â Â and our example gallery > > >Â Â Â http://scikit-image.org/docs/dev/auto_examples/ > > >Â Â Â This release includes new features such as image inpainting, seam > > >Â Â Â carving, image comparison metrics, and a parallelization framework > based > > >Â Â Â on dask. The release has also improved the support of 3-D images, > with > > >Â Â Â 3-D skeletonization, 3-D phantom data. and partial support of > > >Â Â Â measure.regionprops for 3-D images. Also note that the handling of > > >Â Â Â background pixels by measure.label, a function labeling connected > > >Â Â Â components, has changed to be consistent with scipy.ndimage.label. > > >Â Â Â For this release, we merged over 200 pull requests from 64 > contributors, > > >Â Â Â with bug fixes, cleanups, improved documentation and new features. > > >Â Â Â Release notes are available on > > >Â Â Â http://scikit-image.org/docs/0.12.x/ > release_notes_and_installation.html# > > >Â Â Â release-notes > > >Â Â Â and include a more detailed list of changes, and the complete list > of > > >Â Â Â contributors to this release. > > >Â Â Â The release can be downloaded on PyPi > > >Â Â Â https://pypi.python.org/pypi/scikit-image or directly installed > using pip > > >Â Â Â pip install --upgrade scikit-image > > >Â Â Â Please let us know any issues you might have on the issue tracker > > >Â Â Â https://github.com/scikit-image/scikit-image/issues > > >Â Â Â Many thanks to all the developers who made this release possible, > and a > > >Â Â Â warm welcome to our new contributors. > > >Â Â Â Happy image processing! > > >Â Â Â The scikit-image team

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release: scikit-image 0.12 is out!
by Emmanuelle Gouillart 28 Apr '16

28 Apr '16

Announcement: scikit-image 0.12 =============================== The scikit-image team is very pleased to announce the release of version 0.12 of scikit-image. scikit-image is an image processing toolbox for Python and SciPy, that includes algorithms for segmentation, geometric transformations, color space manipulation, analysis, filtering, morphology, feature detection, and more, for 2-D and 3-D (sometimes n-D) images. For more information, examples, and documentation, please visit our website: http://scikit-image.org and our example gallery http://scikit-image.org/docs/dev/auto_examples/ This release includes new features such as image inpainting, seam carving, image comparison metrics, and a parallelization framework based on dask. The release has also improved the support of 3-D images, with 3-D skeletonization, 3-D phantom data. and partial support of measure.regionprops for 3-D images. Also note that the handling of background pixels by measure.label, a function labeling connected components, has changed to be consistent with scipy.ndimage.label. For this release, we merged over 200 pull requests from 64 contributors, with bug fixes, cleanups, improved documentation and new features. Release notes are available on http://scikit-image.org/docs/0.12.x/release_notes_and_installation.html#rel… and include a more detailed list of changes, and the complete list of contributors to this release. The release can be downloaded on PyPi https://pypi.python.org/pypi/scikit-image or directly installed using pip pip install --upgrade scikit-image Please let us know any issues you might have on the issue tracker https://github.com/scikit-image/scikit-image/issues Many thanks to all the developers who made this release possible, and a warm welcome to our new contributors. Happy image processing! The scikit-image team

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Re: Opinion poll: feedback URL upon import
by Juan Nunez-Iglesias 27 Apr '16

27 Apr '16

-1, as others. The suggestions given so far are good: prominent message on the website, and in the main docstring. Juan. From: 'Kevin Keraudren' via scikit-image <scikit-image(a)googlegroups.com> <scikit-image(a)googlegroups.com> Reply: scikit-image(a)googlegroups.com <scikit-image(a)googlegroups.com> <scikit-image(a)googlegroups.com> Date: 26 April 2016 at 9:49:15 PM To: scikit-image(a)googlegroups.com <scikit-image(a)googlegroups.com> <scikit-image(a)googlegroups.com> Subject: Re: Opinion poll: feedback URL upon import Noisy output at import is bad. In addition to the suggestions previously > made, what about also mentioning the feedback url in the main docstring of > skimage, something like here: > https://github.com/scikit-image/scikit-image/blob/master/skimage/__init__.p… > > On Tue, Apr 26, 2016 at 12:40 PM, Jaidev Deshpande < > deshpande.jaidev(a)gmail.com> wrote: > >> >> >> On Tue, Apr 26, 2016 at 3:40 PM, 'Robin Wilson' via scikit-image < >> scikit-image(a)googlegroups.com> wrote: >> >>> I agree with the others: please don't do this! >>> >>> However, being more obvious about wanting feedback, via the website, >>> mailing list, in conference presentations etc, is definitely a good idea. >>> >>> Robin >>> >>> On Tuesday, 26 April 2016 08:05:42 UTC+1, Christoph wrote: >>>> >>>> Hi, >>>> >>>> I agree with Emma, as a scikit-image user, I would find it annoying. >>>> Especially if it catches on and many other Python packages start doing >>>> the same. >>>> >>>> It’s probably very rare, but if people check the text output of their >>>> library or application and use scikit-image somewhere, this could even >>>> break their test build. >>>> >>>> In Astropy there has also been some discussion about how to get >>>> feedback from users. There the discussion was more along the lines of >>>> wanting to collect info which platform, versions are in use, and which >>>> sub-packages and functions in the Astropy package are used. I.e. there was >>>> discussion about adding some code to send such usage stats info to a >>>> server, like many apps do. This didn’t happen, I think the idea has been >>>> dropped. >>>> >>>> It would be very nice and important to get more feedback from users! >>>> >>>> But it seems to me that asking for it on the website like Emma proposes >>>> or in conversations and presentations might be the safer way. >>>> >>>> Christoph >>>> >>>> >>>> >>>> On 26 Apr 2016, at 08:49, Emmanuelle Gouillart <emmanuelle...(a)nsup.org> >>>> wrote: >>>> >>>> Hi Stéfan >>>> >>>> I'm quite against it, since it's a feature that would push scikit-image >>>> to be more an application and less a self-standing library: we would >>>> like >>>> any other package to be able to import skimage in their code without >>>> bothering about such messages. Indeed, such a message at import is only >>>> useful/relevant for people that use scikit-image deliberately and as an >>>> important part of their workflow, not so much for people that import >>>> skimage in another projects, or that just use a couple of functions of >>>> scikit-image (but it's not the core part of their workflow). I consider >>>> it important for scikit-image to be a versatile block of the ecosystem, >>>> and not only an application at the end of the "food chain". >>>> >>>> We could advertise the feedback form in a different way, for example by >>>> making it very visible on the website. With 20000 unique visitors coming >>>> to the website every month, I hope that we could get some feedback... >>>> >>>> Best, >>>> Emma >>>> >>>> On Mon, Apr 25, 2016 at 11:29:03PM +0000, Stéfan van der Walt wrote: >>>> >>>> Hi all, >>>> >>>> >>>> It has been difficult to discover use cases of scikit-image out in the >>>> wild >>>> (even though I know they are plentiful, and users would excitedly tell >>>> me about >>>> them at conferences once the topic is broached). >>>> >>>> >>>> So, I was wondering if it would be considered bad form to print a >>>> message upon >>>> importing scikit-image, something along the lines of: >>>> >>>> >>>> "Thank you for using scikit-image v0.12! Please help us by telling us >>>> about >>>> your use-case at http://scikit-image.org/feedback?v=0.12.3" >>>> >>>> >>>> Thanks for your feedback, >>>> >>>> >>>> Stéfan >>>> >>>> >>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "scikit-image" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to scikit-image...(a)googlegroups.com. >>>> To post to this group, send an email to scikit...(a)googlegroups.com. >>>> To view this discussion on the web, visit >>>> https://groups.google.com/d/msgid/scikit-image/20160426064948.GB940933%40ph… >>>> . >>>> 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(a)googlegroups.com. >>> To post to this group, send email to scikit-image(a)googlegroups.com. >>> To view this discussion on the web, visit >>> https://groups.google.com/d/msgid/scikit-image/55d7ee35-aae3-458f-8245-1d35… >>> <https://groups.google.com/d/msgid/scikit-image/55d7ee35-aae3-458f-8245-1d35…>. >>> >>> >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> How about posting this message when skimage is installed? It could be >> added to the setup.py script. But that would be visible only for users >> installing skimage from source, since pip / conda / enpkg would most >> probably suppress the message. >> >> Would it make sense to add a message in the LICENSE file? >> >> -- >> JD >> >> -- >> 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(a)googlegroups.com. >> To post to this group, send email to scikit-image(a)googlegroups.com. >> To view this discussion on the web, visit >> https://groups.google.com/d/msgid/scikit-image/CAB%3DsuEkN-VdjQ%3DZ6%3DRXKn… >> <https://groups.google.com/d/msgid/scikit-image/CAB%3DsuEkN-VdjQ%3DZ6%3DRXKn…>. >> >> >> 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(a)googlegroups.com. > To post to this group, send email to scikit-image(a)googlegroups.com. > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/CADe6jSp756gGkgXYhdjvGzzD2q3… > <https://groups.google.com/d/msgid/scikit-image/CADe6jSp756gGkgXYhdjvGzzD2q3…> > . > For more options, visit https://groups.google.com/d/optout. >

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Re: Opinion poll: feedback URL upon import
by Kevin Keraudren 26 Apr '16

26 Apr '16

Noisy output at import is bad. In addition to the suggestions previously made, what about also mentioning the feedback url in the main docstring of skimage, something like here: https://github.com/scikit-image/scikit-image/blob/master/skimage/__init__.p… On Tue, Apr 26, 2016 at 12:40 PM, Jaidev Deshpande < deshpande.jaidev(a)gmail.com> wrote: > > > On Tue, Apr 26, 2016 at 3:40 PM, 'Robin Wilson' via scikit-image < > scikit-image(a)googlegroups.com> wrote: > >> I agree with the others: please don't do this! >> >> However, being more obvious about wanting feedback, via the website, >> mailing list, in conference presentations etc, is definitely a good idea. >> >> Robin >> >> On Tuesday, 26 April 2016 08:05:42 UTC+1, Christoph wrote: >>> >>> Hi, >>> >>> I agree with Emma, as a scikit-image user, I would find it annoying. >>> Especially if it catches on and many other Python packages start doing >>> the same. >>> >>> It’s probably very rare, but if people check the text output of their >>> library or application and use scikit-image somewhere, this could even >>> break their test build. >>> >>> In Astropy there has also been some discussion about how to get feedback >>> from users. There the discussion was more along the lines of wanting to >>> collect info which platform, versions are in use, and which sub-packages >>> and functions in the Astropy package are used. I.e. there was discussion >>> about adding some code to send such usage stats info to a server, like many >>> apps do. This didn’t happen, I think the idea has been dropped. >>> >>> It would be very nice and important to get more feedback from users! >>> >>> But it seems to me that asking for it on the website like Emma proposes >>> or in conversations and presentations might be the safer way. >>> >>> Christoph >>> >>> >>> >>> On 26 Apr 2016, at 08:49, Emmanuelle Gouillart <emmanuelle...(a)nsup.org> >>> wrote: >>> >>> Hi Stéfan >>> >>> I'm quite against it, since it's a feature that would push scikit-image >>> to be more an application and less a self-standing library: we would like >>> any other package to be able to import skimage in their code without >>> bothering about such messages. Indeed, such a message at import is only >>> useful/relevant for people that use scikit-image deliberately and as an >>> important part of their workflow, not so much for people that import >>> skimage in another projects, or that just use a couple of functions of >>> scikit-image (but it's not the core part of their workflow). I consider >>> it important for scikit-image to be a versatile block of the ecosystem, >>> and not only an application at the end of the "food chain". >>> >>> We could advertise the feedback form in a different way, for example by >>> making it very visible on the website. With 20000 unique visitors coming >>> to the website every month, I hope that we could get some feedback... >>> >>> Best, >>> Emma >>> >>> On Mon, Apr 25, 2016 at 11:29:03PM +0000, Stéfan van der Walt wrote: >>> >>> Hi all, >>> >>> >>> It has been difficult to discover use cases of scikit-image out in the >>> wild >>> (even though I know they are plentiful, and users would excitedly tell >>> me about >>> them at conferences once the topic is broached). >>> >>> >>> So, I was wondering if it would be considered bad form to print a >>> message upon >>> importing scikit-image, something along the lines of: >>> >>> >>> "Thank you for using scikit-image v0.12! Please help us by telling us >>> about >>> your use-case at http://scikit-image.org/feedback?v=0.12.3" >>> >>> >>> Thanks for your feedback, >>> >>> >>> Stéfan >>> >>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "scikit-image" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to scikit-image...(a)googlegroups.com. >>> To post to this group, send an email to scikit...(a)googlegroups.com. >>> To view this discussion on the web, visit >>> https://groups.google.com/d/msgid/scikit-image/20160426064948.GB940933%40ph… >>> . >>> 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(a)googlegroups.com. >> To post to this group, send email to scikit-image(a)googlegroups.com. >> To view this discussion on the web, visit >> https://groups.google.com/d/msgid/scikit-image/55d7ee35-aae3-458f-8245-1d35… >> <https://groups.google.com/d/msgid/scikit-image/55d7ee35-aae3-458f-8245-1d35…> >> . >> >> For more options, visit https://groups.google.com/d/optout. >> > > How about posting this message when skimage is installed? It could be > added to the setup.py script. But that would be visible only for users > installing skimage from source, since pip / conda / enpkg would most > probably suppress the message. > > Would it make sense to add a message in the LICENSE file? > > -- > JD > > -- > 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(a)googlegroups.com. > To post to this group, send email to scikit-image(a)googlegroups.com. > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/CAB%3DsuEkN-VdjQ%3DZ6%3DRXKn… > <https://groups.google.com/d/msgid/scikit-image/CAB%3DsuEkN-VdjQ%3DZ6%3DRXKn…> > . > > For more options, visit https://groups.google.com/d/optout. >

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Re: Opinion poll: feedback URL upon import
by Emmanuelle Gouillart 26 Apr '16

26 Apr '16

Hi StÃ©fan I'm quite against it, since it's a feature that would push scikit-image to be more an application and less a self-standing library: we would like any other package to be able to import skimage in their code without bothering about such messages. Indeed, such a message at import is only useful/relevant for people that use scikit-image deliberately and as an important part of their workflow, not so much for people that import skimage in another projects, or that just use a couple of functions of scikit-image (but it's not the core part of their workflow). I consider it important for scikit-image to be a versatile block of the ecosystem, and not only an application at the end of the "food chain". We could advertise the feedback form in a different way, for example by making it very visible on the website. With 20000 unique visitors coming to the website every month, I hope that we could get some feedback... Best, Emma On Mon, Apr 25, 2016 at 11:29:03PM +0000, StÃ©fan van der Walt wrote: > Hi all, > It has been difficult to discover use cases of scikit-image out in the wild > (even though I know they are plentiful, and users would excitedly tell me about > them at conferences once the topic is broached). > So, I was wondering if it would be considered bad form to print a message upon > importing scikit-image, something along the lines of: > "Thank you for using scikit-image v0.12! Please help us by telling us about > your use-case at http://scikit-image.org/feedback?v=0.12.3" > Thanks for your feedback, > StÃ©fan

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Opinion poll: feedback URL upon import
by Stéfan van der Walt 25 Apr '16

25 Apr '16

Hi all, It has been difficult to discover use cases of scikit-image out in the wild (even though I know they are plentiful, and users would excitedly tell me about them at conferences once the topic is broached). So, I was wondering if it would be considered bad form to print a message upon importing scikit-image, something along the lines of: "Thank you for using scikit-image v0.12! Please help us by telling us about your use-case at http://scikit-image.org/feedback?v=0.12.3" Thanks for your feedback, Stéfan

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ANN: Tutorial at SciPy 2016
by Stéfan van der Walt 25 Apr '16

25 Apr '16

Hi everyone A quick announcement: we'll be giving a scikit-image tutorial at SciPy 2016 this year! So far on the team we have Juan, myself, and Andreas Mueller for machine learning advice. If any of you would like to be involved in preparing and/or delivering material, please let me know. Best regards Stefan

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the spatial aspect ratio in gabor kernel
by Jungle Chan 19 Apr '16

19 Apr '16

There is no parameter "gama(the spatial aspect ratio)" in gabor kernel, may I modify for it?

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Re: skimage.io.Image??
by Emmanuelle Gouillart 18 Apr '16

18 Apr '16

Oops sorry Fernando, and thanks StÃ©fan for sharing a healthy reminder that the deprecation policy is very useful, and should be enforced with care. On Mon, Apr 18, 2016 at 01:03:38PM -0700, StÃ©fan van der Walt wrote: > Hey Fernando (& skimage list, CC'd) > On 18 April 2016 at 01:43, Fernando Perez <fperez(a)lbl.gov> wrote: > > Quick question, where did this go? > > http://scikit-image.org/docs/0.11.x/api/skimage.io.html#image > > It's not there in 0.12 and newer, and nowhere do the docs indicate that it > > was removed, moved or otherwise tell me what I should do: > > http://scikit-image.org/docs/dev/api_changes.html#version-0-12 > This was an oversight; we have a two release deprecation policy (with > inline warnings + mentions in the docs) which was not followed in this > case. The internal API change was documented in the v0.9 api_changes > document, but unfortunately not the rest. > > We have an example in IPython that uses it: > > https://github.com/ipython/ipywidgets/blob/master/docs/source/examples/Imag… > I spoke to Brian several months ago to fix the issue after this came > to our attention, but I guess the changes have not made their way > through to ipywidgets. > > Any help appreciated (and you shouldn't remove classes like this from the > > API without deprecation period, warning or mention in the docs :) > Of course, you are right, this type of thing should never, ever > happen--I apologize for the confusion and wasted time. > The Image class, just like most other numpy subclasses, turned out to > be a mistake. It wouldn't carry through the whole pipeline, and ended > up causing more confusion than what it helped. > I've factored out the source and attached it here, in case that is of some help: > from image import Image > from skimage import data > cat = data.chelsea() > Image(cat) > StÃ©fan

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Re: skimage.io.Image??
by Stéfan van der Walt 18 Apr '16

18 Apr '16

Hey Fernando (& skimage list, CC'd) On 18 April 2016 at 01:43, Fernando Perez <fperez(a)lbl.gov> wrote: > Quick question, where did this go? > > http://scikit-image.org/docs/0.11.x/api/skimage.io.html#image > > It's not there in 0.12 and newer, and nowhere do the docs indicate that it > was removed, moved or otherwise tell me what I should do: > > http://scikit-image.org/docs/dev/api_changes.html#version-0-12 This was an oversight; we have a two release deprecation policy (with inline warnings + mentions in the docs) which was not followed in this case. The internal API change was documented in the v0.9 api_changes document, but unfortunately not the rest. > We have an example in IPython that uses it: > https://github.com/ipython/ipywidgets/blob/master/docs/source/examples/Imag… I spoke to Brian several months ago to fix the issue after this came to our attention, but I guess the changes have not made their way through to ipywidgets. > Any help appreciated (and you shouldn't remove classes like this from the > API without deprecation period, warning or mention in the docs :) Of course, you are right, this type of thing should never, ever happen--I apologize for the confusion and wasted time. The Image class, just like most other numpy subclasses, turned out to be a mistake. It wouldn't carry through the whole pipeline, and ended up causing more confusion than what it helped. I've factored out the source and attached it here, in case that is of some help: from image import Image from skimage import data cat = data.chelsea() Image(cat) Stéfan

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