Mailman 3 August 2016 - scikit-image

Re: Image edge detection
by Dipankar “Dipu” Ganguly 11 Aug '16

11 Aug '16

Your suggestions have been very helpful and allowed me to make good progress. Do you know where I can find the Python source code for the edge filters in MatPlotlib? Thanks. Dipu Dipankar Ganguly Consultant: Strategy/Technology/Commercialization Bothell, WA Cell: 408-203-8814 email: dipugee(a)gmail.com http://www.linkedin.com/in/dipugee > On Aug 9, 2016, at 2:42 PM, Stéfan van der Walt <stefanv(a)berkeley.edu> wrote: > > Hi Dipu > > On 9 August 2016 at 14:40, Dipankar “Dipu” Ganguly <dipugee(a)gmail.com <mailto:dipugee@gmail.com>> 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? > > Stéfan > > -- > 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 <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(a)googlegroups.com <mailto:scikit-image+unsubscribe@googlegroups.com>. > To post to this group, send email to scikit-image(a)googlegroups.com <mailto:scikit-image@googlegroups.com>. > To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/CABDkGQnhpOQemWLzN5G2ACwwXgL… <https://groups.google.com/d/msgid/scikit-image/CABDkGQnhpOQemWLzN5G2ACwwXgL…>. > For more options, visit https://groups.google.com/d/optout <https://groups.google.com/d/optout>.

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Re: Migration to Python 3.x
by Stéfan van der Walt 10 Aug '16

10 Aug '16

Hi Nelle On 9 August 2016 at 18:55, Nelle Varoquaux <nelle.varoquaux(a)gmail.com> wrote: > That implies that even ubuntu users will have to install python from > another source than the package manager. Do you really want this? That > means that only fairly advance python users will be able to use the > latest scikit-image release. > Ubuntu users haven't had the latest scikit-image for quite a while, unfortunately. We are working on fixing that, but not many people have noticed. Stéfan

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Re: Migration to Python 3.x
by Nelle Varoquaux 10 Aug '16

10 Aug '16

On 9 August 2016 at 19:54, Ralf Gommers <ralf.gommers(a)gmail.com> wrote: > > > On Wed, Aug 10, 2016 at 2:46 PM, Nelle Varoquaux <nelle.varoquaux(a)gmail.com> > wrote: >> >> On 9 August 2016 at 19:17, Ralf Gommers <ralf.gommers(a)gmail.com> wrote: >> > >> > >> > On Wed, Aug 10, 2016 at 1:55 PM, Nelle Varoquaux >> > <nelle.varoquaux(a)gmail.com> >> > wrote: >> >> >> >> On 9 August 2016 at 17:28, Juan Nunez-Iglesias <jni.soma(a)gmail.com> >> >> wrote: >> >> > @Emmanuelle I'm probably among the ones pushing hardest for this, and >> >> > I >> >> > can >> >> > tell you, I can't wait for this change in policy, and would be sorely >> >> > disappointed by having to work in an experimental branch of >> >> > scikit-image. >> >> > Both @-matmul and keyword-only arguments are, imho, compelling >> >> > reasons >> >> > to >> >> > switch. (Imagine the amount of fiddling with the API that we could do >> >> > with >> >> > keyword-only arguments, without the annoying deprecation cycle!) >> >> > >> >> > @Ralf I would argue in favour of 3.5, for the above reasons and >> >> > because >> >> > anyone who had the temerity to update to 3.4 is very likely to >> >> > subsequently >> >> > move to 3.5. (Self-selected group of early adopters, plus no >> >> > backwards >> >> > incompatibility issues between the two versions.) >> > >> > >> > I agree with this argument, I was just asking to clarify. @ is at least >> > something interesting that's specifically added for scientific users, so >> > imho 3.5 is the first 3.x release where in some cases the benefits may >> > start >> > to be worth the costs. >> > >> >> >> >> That implies that even ubuntu users will have to install python from >> >> another source than the package manager. Do you really want this? That >> >> means that only fairly advance python users will be able to use the >> >> latest scikit-image release. >> > >> > >> > In the grand scheme of things, does Ubuntu matter much for this >> > decision? >> > There are way more Windows and OS X users, so if it's OK for them (which >> > is >> > not a given) then it should also be OK for those fewer and on average >> > more >> > computer-literate Ubuntu users. >> >> I don't have a good overview of what OS people are using, but in the >> different research facilities I've worked or visited, it was always >> linux based, and users where not really tech-savy. I checked on all of >> the servers (UW's genome science, the Curie institute, UC Berkeley's >> stats department, the Mines' machine learning computing facilities.) I >> have access to, none have python3.5. Some of these servers are >> "offline", thus conda is useless. All of these research institutes >> have teams that use in some way image processing. >> >> I'll just also mentionned that we had a keynote at scipy this year >> mentionning she was using python because she just did not have the >> time anymore to code in C++ and Java. These are the kind of people >> that may be using scikit-image, that may be interested in the latest >> version of the package, and yet just not have the time to compile >> python3.5 from scratch on an outdated server. > > > Fair enough, but there are likely much more outdated servers with Python 2.7 > than with Python 3.4 on them ..... Well… I think it is better to keep python2.7 support :) All the clusters I have access to but 1 has python3. The oldest one is a red hat based cluster with python2.6 (which was python2.3 not so long ago). N > > Ralf > > -- > 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/CABL7CQjye5g5jppRk1hej2g2P3V…. > > For more options, visit https://groups.google.com/d/optout.

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Re: Migration to Python 3.x
by Ralf Gommers 10 Aug '16

10 Aug '16

On Wed, Aug 10, 2016 at 2:46 PM, Nelle Varoquaux <nelle.varoquaux(a)gmail.com> wrote: > On 9 August 2016 at 19:17, Ralf Gommers <ralf.gommers(a)gmail.com> wrote: > > > > > > On Wed, Aug 10, 2016 at 1:55 PM, Nelle Varoquaux < > nelle.varoquaux(a)gmail.com> > > wrote: > >> > >> On 9 August 2016 at 17:28, Juan Nunez-Iglesias <jni.soma(a)gmail.com> > wrote: > >> > @Emmanuelle I'm probably among the ones pushing hardest for this, and > I > >> > can > >> > tell you, I can't wait for this change in policy, and would be sorely > >> > disappointed by having to work in an experimental branch of > >> > scikit-image. > >> > Both @-matmul and keyword-only arguments are, imho, compelling reasons > >> > to > >> > switch. (Imagine the amount of fiddling with the API that we could do > >> > with > >> > keyword-only arguments, without the annoying deprecation cycle!) > >> > > >> > @Ralf I would argue in favour of 3.5, for the above reasons and > because > >> > anyone who had the temerity to update to 3.4 is very likely to > >> > subsequently > >> > move to 3.5. (Self-selected group of early adopters, plus no backwards > >> > incompatibility issues between the two versions.) > > > > > > I agree with this argument, I was just asking to clarify. @ is at least > > something interesting that's specifically added for scientific users, so > > imho 3.5 is the first 3.x release where in some cases the benefits may > start > > to be worth the costs. > > > >> > >> That implies that even ubuntu users will have to install python from > >> another source than the package manager. Do you really want this? That > >> means that only fairly advance python users will be able to use the > >> latest scikit-image release. > > > > > > In the grand scheme of things, does Ubuntu matter much for this decision? > > There are way more Windows and OS X users, so if it's OK for them (which > is > > not a given) then it should also be OK for those fewer and on average > more > > computer-literate Ubuntu users. > > I don't have a good overview of what OS people are using, but in the > different research facilities I've worked or visited, it was always > linux based, and users where not really tech-savy. I checked on all of > the servers (UW's genome science, the Curie institute, UC Berkeley's > stats department, the Mines' machine learning computing facilities.) I > have access to, none have python3.5. Some of these servers are > "offline", thus conda is useless. All of these research institutes > have teams that use in some way image processing. > > I'll just also mentionned that we had a keynote at scipy this year > mentionning she was using python because she just did not have the > time anymore to code in C++ and Java. These are the kind of people > that may be using scikit-image, that may be interested in the latest > version of the package, and yet just not have the time to compile > python3.5 from scratch on an outdated server. > Fair enough, but there are likely much more outdated servers with Python 2.7 than with Python 3.4 on them ..... Ralf

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Re: Migration to Python 3.x
by Nelle Varoquaux 10 Aug '16

10 Aug '16

On 9 August 2016 at 19:17, Ralf Gommers <ralf.gommers(a)gmail.com> wrote: > > > On Wed, Aug 10, 2016 at 1:55 PM, Nelle Varoquaux <nelle.varoquaux(a)gmail.com> > wrote: >> >> On 9 August 2016 at 17:28, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: >> > @Emmanuelle I'm probably among the ones pushing hardest for this, and I >> > can >> > tell you, I can't wait for this change in policy, and would be sorely >> > disappointed by having to work in an experimental branch of >> > scikit-image. >> > Both @-matmul and keyword-only arguments are, imho, compelling reasons >> > to >> > switch. (Imagine the amount of fiddling with the API that we could do >> > with >> > keyword-only arguments, without the annoying deprecation cycle!) >> > >> > @Ralf I would argue in favour of 3.5, for the above reasons and because >> > anyone who had the temerity to update to 3.4 is very likely to >> > subsequently >> > move to 3.5. (Self-selected group of early adopters, plus no backwards >> > incompatibility issues between the two versions.) > > > I agree with this argument, I was just asking to clarify. @ is at least > something interesting that's specifically added for scientific users, so > imho 3.5 is the first 3.x release where in some cases the benefits may start > to be worth the costs. > >> >> That implies that even ubuntu users will have to install python from >> another source than the package manager. Do you really want this? That >> means that only fairly advance python users will be able to use the >> latest scikit-image release. > > > In the grand scheme of things, does Ubuntu matter much for this decision? > There are way more Windows and OS X users, so if it's OK for them (which is > not a given) then it should also be OK for those fewer and on average more > computer-literate Ubuntu users. I don't have a good overview of what OS people are using, but in the different research facilities I've worked or visited, it was always linux based, and users where not really tech-savy. I checked on all of the servers (UW's genome science, the Curie institute, UC Berkeley's stats department, the Mines' machine learning computing facilities.) I have access to, none have python3.5. Some of these servers are "offline", thus conda is useless. All of these research institutes have teams that use in some way image processing. I'll just also mentionned that we had a keynote at scipy this year mentionning she was using python because she just did not have the time anymore to code in C++ and Java. These are the kind of people that may be using scikit-image, that may be interested in the latest version of the package, and yet just not have the time to compile python3.5 from scratch on an outdated server. N > > Ralf > > -- > 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/CABL7CQhEaD0uy0SyrcNO_j%2BDs…. > > For more options, visit https://groups.google.com/d/optout.

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Re: Migration to Python 3.x
by Ralf Gommers 10 Aug '16

10 Aug '16

On Wed, Aug 10, 2016 at 1:55 PM, Nelle Varoquaux <nelle.varoquaux(a)gmail.com> wrote: > On 9 August 2016 at 17:28, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: > > @Emmanuelle I'm probably among the ones pushing hardest for this, and I > can > > tell you, I can't wait for this change in policy, and would be sorely > > disappointed by having to work in an experimental branch of scikit-image. > > Both @-matmul and keyword-only arguments are, imho, compelling reasons to > > switch. (Imagine the amount of fiddling with the API that we could do > with > > keyword-only arguments, without the annoying deprecation cycle!) > > > > @Ralf I would argue in favour of 3.5, for the above reasons and because > > anyone who had the temerity to update to 3.4 is very likely to > subsequently > > move to 3.5. (Self-selected group of early adopters, plus no backwards > > incompatibility issues between the two versions.) > I agree with this argument, I was just asking to clarify. @ is at least something interesting that's specifically added for scientific users, so imho 3.5 is the first 3.x release where in some cases the benefits may start to be worth the costs. > That implies that even ubuntu users will have to install python from > another source than the package manager. Do you really want this? That > means that only fairly advance python users will be able to use the > latest scikit-image release. > In the grand scheme of things, does Ubuntu matter much for this decision? There are way more Windows and OS X users, so if it's OK for them (which is not a given) then it should also be OK for those fewer and on average more computer-literate Ubuntu users. Ralf

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Re: Migration to Python 3.x
by Nelle Varoquaux 10 Aug '16

10 Aug '16

On 9 August 2016 at 17:28, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: > @Emmanuelle I'm probably among the ones pushing hardest for this, and I can > tell you, I can't wait for this change in policy, and would be sorely > disappointed by having to work in an experimental branch of scikit-image. > Both @-matmul and keyword-only arguments are, imho, compelling reasons to > switch. (Imagine the amount of fiddling with the API that we could do with > keyword-only arguments, without the annoying deprecation cycle!) > > @Ralf I would argue in favour of 3.5, for the above reasons and because > anyone who had the temerity to update to 3.4 is very likely to subsequently > move to 3.5. (Self-selected group of early adopters, plus no backwards > incompatibility issues between the two versions.) That implies that even ubuntu users will have to install python from another source than the package manager. Do you really want this? That means that only fairly advance python users will be able to use the latest scikit-image release. > > Juan. > > On Wed, Aug 10, 2016 at 8:14 AM, Stéfan van der Walt <stefanv(a)berkeley.edu> > wrote: >> >> Hi Ralf >> >> On 9 August 2016 at 15:09, Ralf Gommers <ralf.gommers(a)gmail.com> wrote: >>> >>> Hi Stefan, do you propose then to drop Python 3.4 at the same time (@ is >>> >= 3.5)? >> >> >> Yes, I guess I am. But if that's too much of a stretch, I will be open to >> >= 3.4. >> >> 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+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/CABDkGQmSC7Q7jZJDBuhutj2PXjQ…. >> >> 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/CA%2BJHcKSM0sERcWwSMXc4dk6uh…. > > For more options, visit https://groups.google.com/d/optout.

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Re: Migration to Python 3.x
by Juan Nunez-Iglesias 10 Aug '16

10 Aug '16

@Emmanuelle I'm probably among the ones pushing hardest for this, and I can tell you, I can't wait for this change in policy, and would be sorely disappointed by having to work in an experimental branch of scikit-image. Both @-matmul and keyword-only arguments are, imho, compelling reasons to switch. (Imagine the amount of fiddling with the API that we could do with keyword-only arguments, without the annoying deprecation cycle!) @Ralf I would argue in favour of 3.5, for the above reasons and because anyone who had the temerity to update to 3.4 is very likely to subsequently move to 3.5. (Self-selected group of early adopters, plus no backwards incompatibility issues between the two versions.) Juan. On Wed, Aug 10, 2016 at 8:14 AM, Stéfan van der Walt <stefanv(a)berkeley.edu> wrote: > Hi Ralf > > On 9 August 2016 at 15:09, Ralf Gommers <ralf.gommers(a)gmail.com> wrote: > >> Hi Stefan, do you propose then to drop Python 3.4 at the same time (@ is >> >= 3.5)? >> > > Yes, I guess I am. But if that's too much of a stretch, I will be open to > >= 3.4. > > 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+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/CABDkGQmSC7Q7jZJDBuhutj2PXjQTDGDirxafVw-GFuqcN%3DK1_A% > 40mail.gmail.com > <https://groups.google.com/d/msgid/scikit-image/CABDkGQmSC7Q7jZJDBuhutj2PXjQ…> > . > > For more options, visit https://groups.google.com/d/optout. >

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Re: Migration to Python 3.x
by Stéfan van der Walt 09 Aug '16

09 Aug '16

Hi Ralf On 9 August 2016 at 15:09, Ralf Gommers <ralf.gommers(a)gmail.com> wrote: > Hi Stefan, do you propose then to drop Python 3.4 at the same time (@ is > >= 3.5)? > Yes, I guess I am. But if that's too much of a stretch, I will be open to >= 3.4. Stéfan

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Re: Migration to Python 3.x
by Ralf Gommers 09 Aug '16

09 Aug '16

On Wed, Aug 10, 2016 at 9:58 AM, Stéfan van der Walt <stefanv(a)berkeley.edu> wrote: > Hi Emmanuelle > > > On 9 August 2016 at 14:44, Emmanuelle Gouillart < > emmanuelle.gouillart(a)nsup.org> wrote: > > >> It may be a silly idea, but can't we do it the other way around, that is >> have an experimental branch where developers who wish to write >> Python3-only code can work, and in which commits to master are merged if >> they are Python 3 compatible? It could give us some time to evaluate >> whether most developers want to write code that is not compatible with >> Python 2. >> > > I don't think that's a silly idea, but I also don't think that addresses > two of the points I raised: > > - Remove developer overhead associated with keeping both Python 2 and > 3-isms in mind > > I'd like developers to start thinking in Python 3, not the other way > around. Barriers for Python 3 implementations should be removed, not > raised, given that that's the direction we'll have to move eventually. > > - Utilize new language features such as the @-operator and required > keyword arguments > > These are not available unless we make Python 3 the default. > Hi Stefan, do you propose then to drop Python 3.4 at the same time (@ is >= 3.5)? Ralf

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