scikit-image October 2013

scikit-image@python.org

27 participants
74 discussions

Re: umfpack error
by Ralf Gommers 04 Oct '13

04 Oct '13

On Fri, Oct 4, 2013 at 1:33 PM, Juan Nunez-Iglesias <jni.soma(a)gmail.com>wrote: > On Fri, Oct 4, 2013 at 8:59 PM, Johannes Schönberger <jsch(a)demuc.de>wrote: > >> Are you sure you have SWIG installed? >> > > I wasn't and I didn't. =) > > Bloody hell scipy takes a long time to build. =) > $ time python setup.py build_ext -i real 12m6.843s user 6m3.244s sys 0m13.124s $ time ../Bento/bentomaker build -i -j # -j == parallel build (on 4 cores here) real 1m46.466s user 2m54.628s sys 0m10.900s Blame distutils (and start using Bento) :) Ralf > 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(a)googlegroups.com. > For more options, visit https://groups.google.com/groups/opt_out. >

1 0

Re: large PyWavelets update, please test
by Ralf Gommers 04 Oct '13

04 Oct '13

On Fri, Oct 4, 2013 at 1:56 PM, Stuart Mumford <stuart(a)mumford.me.uk> wrote: > Hi, > > Thanks for your help. Would this be worthwhile doing? i.e. is this code > something that scipy would appreciate if we could re-licence it? > Adding the missing parts in scipy would definitely be worth doing imho. The chisquare stuff and Morlet wavelet are already in scipy, DOG and Paul wavelets can certainly be added. Then there's the FFT-based cwt function to be added. The Torrence code comments aren't very clear, but it's the Matlab cwtft function as far as I can tell: http://www.mathworks.nl/help/wavelet/ref/cwtft.html. It could probably be added with the same name. Ralf > > Stuart > > > On 4 October 2013 12:09, Ralf Gommers <ralf.gommers(a)gmail.com> wrote: > >> >> >> >> On Fri, Oct 4, 2013 at 1:04 PM, Ralf Gommers <ralf.gommers(a)gmail.com>wrote: >> >>> >>> >>> >>> On Fri, Oct 4, 2013 at 12:46 PM, Stuart Mumford <stuart(a)mumford.me.uk>wrote: >>> >>>> Hi Ralf, >>>> >>>> I realise the license is pants! We are making efforts to contact the >>>> author and persuade him to change it! ;) >>>> >>> >>> The original author can't do this, you also need at least permission >>> from Torrence/Compo as well as from these guys: >>> http://noc.ac.uk/using-science/crosswavelet-wavelet-coherence. And >>> maybe also from A. Brazhe; can't check because the link to his site is >>> dead. So the odds you can get the license changed seem on the low side. >>> >> >> Found the Brazhe code, it's (now?) GPL licensed: >> https://pypi.python.org/pypi/swan >> >> Ralf >> >> >>> >>> The reason we are looking at this is it has all the features my friend >>>> needed, so it seemed easier (at least from a getting work done perspective) >>>> to start with this code, which also happened to be a (far to direct) >>>> implementation of the IDL code he was having to use before. >>>> >>>> While it would be nice to build some or all of this into a bigger >>>> package, at the end of the day just having a decent Python implementation >>>> of the C. Torrence and G. P. Compo wavelet code will be yet another thing >>>> people don't need IDL for. >>>> >>> >>> I just checked the Matlab code from >>> http://paos.colorado.edu/research/wavelets/ (I don't speak IDL) and >>> it's not a lot of code nor is it very complicated. What I would suggest is >>> to contact Torrence and Compo directly to see if they're willing to change >>> to a BSD license, and otherwise just reimplement the algorithm based on >>> their paper. >>> >>> >>>> >>>> Stuart >>>> >>>> P.S. I am a solar physicist and IDL is everywhere *shudders* >>>> >>> >>> :) >>> >>> Cheers, >>> Ralf >>> >>> >>>> >>>> >>>> On 4 October 2013 11:41, Ralf Gommers <ralf.gommers(a)gmail.com> wrote: >>>> >>>>> >>>>> >>>>> >>>>> On Fri, Oct 4, 2013 at 12:32 PM, Stuart Mumford <stuart(a)mumford.me.uk>wrote: >>>>> >>>>>> Hello, >>>>>> >>>>>> On the topic of wavelet's I am involved in a very small scale effort >>>>>> to tidy up this continuous wavelet package, with (if we can contact the >>>>>> original author) the eventual aim of making it useful and potentially a >>>>>> part of some larger package (scipy?). >>>>>> >>>>>> https://github.com/nabobalis/kPyWavelet >>>>>> >>>>> >>>>> Hi Stuart, that code has a license that's incompatible with both BSD >>>>> and GPL licenses so it's pretty much useless. The amount of code there is >>>>> not much more than what's already in scipy.signal.wavelets, so improving >>>>> the scipy cwt code would probably be a better idea. >>>>> >>>>> Ralf >>>>> >>>>> >>>>> >>>>>> >>>>>> Stuart >>>>>> >>>>>> >>>>>> On 4 October 2013 09:15, François Boulogne <fboulogne(a)sciunto.org>wrote: >>>>>> >>>>>>> Dear skimagers, >>>>>>> >>>>>>> >>>>>>> With Ralf, we initiated a "friendly" fork of pywavelet for a future >>>>>>> inclusion in scipy and David joined us in this work. We improved the >>>>>>> doc, removed old-fashioned codes and we are trying now to add tests. >>>>>>> We started this because I was considering this ticket: >>>>>>> https://github.com/scikit-image/scikit-image/issues/602 >>>>>>> Indeed, I believe wavelets may be useful for scikit-image. Instead of >>>>>>> requiring a new dependency, I thought it is much more valuable to >>>>>>> integrate the code in scipy and this is now in the workplan for >>>>>>> scipy1.0. >>>>>>> >>>>>>> If some of you used pywavelet before, we would be grateful to you if >>>>>>> you >>>>>>> can check your code against the fork. It must be fully compatible >>>>>>> with >>>>>>> pywavelets. >>>>>>> >>>>>>> Thanks! >>>>>>> Cheers. >>>>>>> François. >>>>>>> >>>>>>> >>>>>>> -------- Message original -------- >>>>>>> Sujet: large PyWavelets update, please test >>>>>>> Date : Tue, 1 Oct 2013 17:56:36 +0200 >>>>>>> De : Ralf Gommers <ralf.gommers(a)gmail.com> >>>>>>> Pour : pywavelets(a)googlegroups.com >>>>>>> Copie à : François Boulogne <fboulogne(a)sciunto.org>, >>>>>>> david.menendez.hurtado(a)scilifelab.se >>>>>>> >>>>>>> >>>>>>> >>>>>>> Hi all, >>>>>>> >>>>>>> https://github.com/nigma/pywt/pull/7 contains a large refactoring of >>>>>>> PyWavelets, with contributions from Francois Boulogne, David Menendez >>>>>>> Hurtado and myself. Main feature is support for Python 3 (single code >>>>>>> base). Other changes are: >>>>>>> >>>>>>> - Numpy style docstrings for all public functions >>>>>>> - A unit test suite with reasonable coverage (see >>>>>>> https://coveralls.io/r/rgommers/pywt) >>>>>>> - PEP8 and Numpy C code standard compliance >>>>>>> - Changes to source tree layout, build setup, Numpy interfaces and C >>>>>>> and >>>>>>> Cython templating to more standard styles. >>>>>>> >>>>>>> This set of changes is supposed to be fully backwards compatible. >>>>>>> They >>>>>>> were quite invasive though (~150 commits), so there's a decent chance >>>>>>> that some things not covered by the test suite were broken in the >>>>>>> process. To catch those now, it would be very helpful if people could >>>>>>> test their own code against either use the PR or the master branch of >>>>>>> https://github.com/rgommers/pywt. >>>>>>> >>>>>>> While we've kept full backwards compatibility so far, we've also >>>>>>> compiled a list of things that could be improved in the current API: >>>>>>> https://github.com/rgommers/pywt/issues/38. Please add suggestions >>>>>>> there >>>>>>> if you have them. >>>>>>> >>>>>>> Cheers, >>>>>>> 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. >>>>>>> For more options, visit https://groups.google.com/groups/opt_out. >>>>>>> >>>>>> >>>>>> -- >>>>>> 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. >>>>>> For more options, visit https://groups.google.com/groups/opt_out. >>>>>> >>>>> >>>>> -- >>>>> 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. >>>>> For more options, visit https://groups.google.com/groups/opt_out. >>>>> >>>> >>>> -- >>>> 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. >>>> For more options, visit https://groups.google.com/groups/opt_out. >>>> >>> >>> >> -- >> 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. >> For more options, visit https://groups.google.com/groups/opt_out. >> > > -- > 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. > For more options, visit https://groups.google.com/groups/opt_out. >

1 0

Re: large PyWavelets update, please test
by Stuart Mumford 04 Oct '13

04 Oct '13

Hi, Thanks for your help. Would this be worthwhile doing? i.e. is this code something that scipy would appreciate if we could re-licence it? Stuart On 4 October 2013 12:09, Ralf Gommers <ralf.gommers(a)gmail.com> wrote: > > > > On Fri, Oct 4, 2013 at 1:04 PM, Ralf Gommers <ralf.gommers(a)gmail.com>wrote: > >> >> >> >> On Fri, Oct 4, 2013 at 12:46 PM, Stuart Mumford <stuart(a)mumford.me.uk>wrote: >> >>> Hi Ralf, >>> >>> I realise the license is pants! We are making efforts to contact the >>> author and persuade him to change it! ;) >>> >> >> The original author can't do this, you also need at least permission from >> Torrence/Compo as well as from these guys: >> http://noc.ac.uk/using-science/crosswavelet-wavelet-coherence. And maybe >> also from A. Brazhe; can't check because the link to his site is dead. So >> the odds you can get the license changed seem on the low side. >> > > Found the Brazhe code, it's (now?) GPL licensed: > https://pypi.python.org/pypi/swan > > Ralf > > >> >> The reason we are looking at this is it has all the features my friend >>> needed, so it seemed easier (at least from a getting work done perspective) >>> to start with this code, which also happened to be a (far to direct) >>> implementation of the IDL code he was having to use before. >>> >>> While it would be nice to build some or all of this into a bigger >>> package, at the end of the day just having a decent Python implementation >>> of the C. Torrence and G. P. Compo wavelet code will be yet another thing >>> people don't need IDL for. >>> >> >> I just checked the Matlab code from >> http://paos.colorado.edu/research/wavelets/ (I don't speak IDL) and it's >> not a lot of code nor is it very complicated. What I would suggest is to >> contact Torrence and Compo directly to see if they're willing to change to >> a BSD license, and otherwise just reimplement the algorithm based on their >> paper. >> >> >>> >>> Stuart >>> >>> P.S. I am a solar physicist and IDL is everywhere *shudders* >>> >> >> :) >> >> Cheers, >> Ralf >> >> >>> >>> >>> On 4 October 2013 11:41, Ralf Gommers <ralf.gommers(a)gmail.com> wrote: >>> >>>> >>>> >>>> >>>> On Fri, Oct 4, 2013 at 12:32 PM, Stuart Mumford <stuart(a)mumford.me.uk>wrote: >>>> >>>>> Hello, >>>>> >>>>> On the topic of wavelet's I am involved in a very small scale effort >>>>> to tidy up this continuous wavelet package, with (if we can contact the >>>>> original author) the eventual aim of making it useful and potentially a >>>>> part of some larger package (scipy?). >>>>> >>>>> https://github.com/nabobalis/kPyWavelet >>>>> >>>> >>>> Hi Stuart, that code has a license that's incompatible with both BSD >>>> and GPL licenses so it's pretty much useless. The amount of code there is >>>> not much more than what's already in scipy.signal.wavelets, so improving >>>> the scipy cwt code would probably be a better idea. >>>> >>>> Ralf >>>> >>>> >>>> >>>>> >>>>> Stuart >>>>> >>>>> >>>>> On 4 October 2013 09:15, François Boulogne <fboulogne(a)sciunto.org>wrote: >>>>> >>>>>> Dear skimagers, >>>>>> >>>>>> >>>>>> With Ralf, we initiated a "friendly" fork of pywavelet for a future >>>>>> inclusion in scipy and David joined us in this work. We improved the >>>>>> doc, removed old-fashioned codes and we are trying now to add tests. >>>>>> We started this because I was considering this ticket: >>>>>> https://github.com/scikit-image/scikit-image/issues/602 >>>>>> Indeed, I believe wavelets may be useful for scikit-image. Instead of >>>>>> requiring a new dependency, I thought it is much more valuable to >>>>>> integrate the code in scipy and this is now in the workplan for >>>>>> scipy1.0. >>>>>> >>>>>> If some of you used pywavelet before, we would be grateful to you if >>>>>> you >>>>>> can check your code against the fork. It must be fully compatible with >>>>>> pywavelets. >>>>>> >>>>>> Thanks! >>>>>> Cheers. >>>>>> François. >>>>>> >>>>>> >>>>>> -------- Message original -------- >>>>>> Sujet: large PyWavelets update, please test >>>>>> Date : Tue, 1 Oct 2013 17:56:36 +0200 >>>>>> De : Ralf Gommers <ralf.gommers(a)gmail.com> >>>>>> Pour : pywavelets(a)googlegroups.com >>>>>> Copie à : François Boulogne <fboulogne(a)sciunto.org>, >>>>>> david.menendez.hurtado(a)scilifelab.se >>>>>> >>>>>> >>>>>> >>>>>> Hi all, >>>>>> >>>>>> https://github.com/nigma/pywt/pull/7 contains a large refactoring of >>>>>> PyWavelets, with contributions from Francois Boulogne, David Menendez >>>>>> Hurtado and myself. Main feature is support for Python 3 (single code >>>>>> base). Other changes are: >>>>>> >>>>>> - Numpy style docstrings for all public functions >>>>>> - A unit test suite with reasonable coverage (see >>>>>> https://coveralls.io/r/rgommers/pywt) >>>>>> - PEP8 and Numpy C code standard compliance >>>>>> - Changes to source tree layout, build setup, Numpy interfaces and C >>>>>> and >>>>>> Cython templating to more standard styles. >>>>>> >>>>>> This set of changes is supposed to be fully backwards compatible. They >>>>>> were quite invasive though (~150 commits), so there's a decent chance >>>>>> that some things not covered by the test suite were broken in the >>>>>> process. To catch those now, it would be very helpful if people could >>>>>> test their own code against either use the PR or the master branch of >>>>>> https://github.com/rgommers/pywt. >>>>>> >>>>>> While we've kept full backwards compatibility so far, we've also >>>>>> compiled a list of things that could be improved in the current API: >>>>>> https://github.com/rgommers/pywt/issues/38. Please add suggestions >>>>>> there >>>>>> if you have them. >>>>>> >>>>>> Cheers, >>>>>> 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. >>>>>> For more options, visit https://groups.google.com/groups/opt_out. >>>>>> >>>>> >>>>> -- >>>>> 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. >>>>> For more options, visit https://groups.google.com/groups/opt_out. >>>>> >>>> >>>> -- >>>> 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. >>>> For more options, visit https://groups.google.com/groups/opt_out. >>>> >>> >>> -- >>> 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. >>> For more options, visit https://groups.google.com/groups/opt_out. >>> >> >> > -- > 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. > For more options, visit https://groups.google.com/groups/opt_out. >

1 0

Re: umfpack error
by Johannes Schönberger 04 Oct '13

04 Oct '13

Are you sure you have SWIG installed? Am 04.10.2013 um 12:49 schrieb Juan Nunez-Iglesias <jni.soma(a)gmail.com>: > Just for future reference, and because it wasn't immediately obvious from googling: the umfpack headers in Ubuntu 13.04 are in the package libsuitesparse-dev. > > But now the scipy build fails with some weird error. Hmmm. > > building extension "scipy.sparse.linalg.dsolve.umfpack.__umfpack" sources > > creating build/src.linux-x86_64-2.7/scipy/sparse/linalg/dsolve > > creating build/src.linux-x86_64-2.7/scipy/sparse/linalg/dsolve/umfpack > > adding 'scipy/sparse/linalg/dsolve/umfpack/umfpack.i' to sources. > > swig: scipy/sparse/linalg/dsolve/umfpack/umfpack.i > > swig -python -I/usr/include/suitesparse -I/usr/include/suitesparse -I/usr/include/suitesparse -o build/src.linux-x86_64-2.7/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c -outdir build/src.linux-x86_64-2.7/scipy/sparse/linalg/dsolve/umfpack scipy/sparse/linalg/dsolve/umfpack/umfpack.i > > unable to execute swig: No such file or directory > > error: command 'swig' failed with exit status 1 > > > > > On Fri, Oct 4, 2013 at 2:39 PM, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: > Thanks Josh for the detailed response and discussion! I think you're absolutely right that it should be suppressed if pyamg is available. And it's probably worth getting that in before the release. Happy to tackle this. > > Juan. > > PS: I'm mostly on OSX, with some Linux on the side. =) > > > On Fri, Oct 4, 2013 at 9:17 AM, Josh Warner <silvertrumpet999(a)gmail.com> wrote: > Final note - umfpack enables mode='cg' in random_walker, which is better than brute force but not the fastest or most efficient mode. The multi-grid preconditioned conjugate gradient method is: mode='cg_mg'. This is enabled by pyamg, which is independent of umfpack and is considerably easier to install and use than the method I just described. > > Come to think of it, we probably should suppress that warning if import pyamg works. It incorrectly implies the user doesn't have the fastest mode available. > > On Thursday, October 3, 2013 1:21:43 AM UTC-5, Juan Nunez-Iglesias wrote: > > > > Hi guys, > > How do I build scipy with umfpack to silence this error: > > Exception AttributeError: "'UmfpackContext' object has no attribute '_symbolic'" in <bound method UmfpackContext.__del__ of <scipy.sparse.linalg.dsolve.umfpack.umfpack.UmfpackContext object at 0x101b62050>> ignored > and speed up random_walker? I've just been doing a pip install scipy till now. > > 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(a)googlegroups.com. > For more options, visit https://groups.google.com/groups/opt_out. > > > > -- > 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. > For more options, visit https://groups.google.com/groups/opt_out.

2 1

Re: large PyWavelets update, please test
by Ralf Gommers 04 Oct '13

04 Oct '13

On Fri, Oct 4, 2013 at 1:04 PM, Ralf Gommers <ralf.gommers(a)gmail.com> wrote: > > > > On Fri, Oct 4, 2013 at 12:46 PM, Stuart Mumford <stuart(a)mumford.me.uk>wrote: > >> Hi Ralf, >> >> I realise the license is pants! We are making efforts to contact the >> author and persuade him to change it! ;) >> > > The original author can't do this, you also need at least permission from > Torrence/Compo as well as from these guys: > http://noc.ac.uk/using-science/crosswavelet-wavelet-coherence. And maybe > also from A. Brazhe; can't check because the link to his site is dead. So > the odds you can get the license changed seem on the low side. > Found the Brazhe code, it's (now?) GPL licensed: https://pypi.python.org/pypi/swan Ralf > > The reason we are looking at this is it has all the features my friend >> needed, so it seemed easier (at least from a getting work done perspective) >> to start with this code, which also happened to be a (far to direct) >> implementation of the IDL code he was having to use before. >> >> While it would be nice to build some or all of this into a bigger >> package, at the end of the day just having a decent Python implementation >> of the C. Torrence and G. P. Compo wavelet code will be yet another thing >> people don't need IDL for. >> > > I just checked the Matlab code from > http://paos.colorado.edu/research/wavelets/ (I don't speak IDL) and it's > not a lot of code nor is it very complicated. What I would suggest is to > contact Torrence and Compo directly to see if they're willing to change to > a BSD license, and otherwise just reimplement the algorithm based on their > paper. > > >> >> Stuart >> >> P.S. I am a solar physicist and IDL is everywhere *shudders* >> > > :) > > Cheers, > Ralf > > >> >> >> On 4 October 2013 11:41, Ralf Gommers <ralf.gommers(a)gmail.com> wrote: >> >>> >>> >>> >>> On Fri, Oct 4, 2013 at 12:32 PM, Stuart Mumford <stuart(a)mumford.me.uk>wrote: >>> >>>> Hello, >>>> >>>> On the topic of wavelet's I am involved in a very small scale effort to >>>> tidy up this continuous wavelet package, with (if we can contact the >>>> original author) the eventual aim of making it useful and potentially a >>>> part of some larger package (scipy?). >>>> >>>> https://github.com/nabobalis/kPyWavelet >>>> >>> >>> Hi Stuart, that code has a license that's incompatible with both BSD and >>> GPL licenses so it's pretty much useless. The amount of code there is not >>> much more than what's already in scipy.signal.wavelets, so improving the >>> scipy cwt code would probably be a better idea. >>> >>> Ralf >>> >>> >>> >>>> >>>> Stuart >>>> >>>> >>>> On 4 October 2013 09:15, François Boulogne <fboulogne(a)sciunto.org>wrote: >>>> >>>>> Dear skimagers, >>>>> >>>>> >>>>> With Ralf, we initiated a "friendly" fork of pywavelet for a future >>>>> inclusion in scipy and David joined us in this work. We improved the >>>>> doc, removed old-fashioned codes and we are trying now to add tests. >>>>> We started this because I was considering this ticket: >>>>> https://github.com/scikit-image/scikit-image/issues/602 >>>>> Indeed, I believe wavelets may be useful for scikit-image. Instead of >>>>> requiring a new dependency, I thought it is much more valuable to >>>>> integrate the code in scipy and this is now in the workplan for >>>>> scipy1.0. >>>>> >>>>> If some of you used pywavelet before, we would be grateful to you if >>>>> you >>>>> can check your code against the fork. It must be fully compatible with >>>>> pywavelets. >>>>> >>>>> Thanks! >>>>> Cheers. >>>>> François. >>>>> >>>>> >>>>> -------- Message original -------- >>>>> Sujet: large PyWavelets update, please test >>>>> Date : Tue, 1 Oct 2013 17:56:36 +0200 >>>>> De : Ralf Gommers <ralf.gommers(a)gmail.com> >>>>> Pour : pywavelets(a)googlegroups.com >>>>> Copie à : François Boulogne <fboulogne(a)sciunto.org>, >>>>> david.menendez.hurtado(a)scilifelab.se >>>>> >>>>> >>>>> >>>>> Hi all, >>>>> >>>>> https://github.com/nigma/pywt/pull/7 contains a large refactoring of >>>>> PyWavelets, with contributions from Francois Boulogne, David Menendez >>>>> Hurtado and myself. Main feature is support for Python 3 (single code >>>>> base). Other changes are: >>>>> >>>>> - Numpy style docstrings for all public functions >>>>> - A unit test suite with reasonable coverage (see >>>>> https://coveralls.io/r/rgommers/pywt) >>>>> - PEP8 and Numpy C code standard compliance >>>>> - Changes to source tree layout, build setup, Numpy interfaces and C >>>>> and >>>>> Cython templating to more standard styles. >>>>> >>>>> This set of changes is supposed to be fully backwards compatible. They >>>>> were quite invasive though (~150 commits), so there's a decent chance >>>>> that some things not covered by the test suite were broken in the >>>>> process. To catch those now, it would be very helpful if people could >>>>> test their own code against either use the PR or the master branch of >>>>> https://github.com/rgommers/pywt. >>>>> >>>>> While we've kept full backwards compatibility so far, we've also >>>>> compiled a list of things that could be improved in the current API: >>>>> https://github.com/rgommers/pywt/issues/38. Please add suggestions >>>>> there >>>>> if you have them. >>>>> >>>>> Cheers, >>>>> 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. >>>>> For more options, visit https://groups.google.com/groups/opt_out. >>>>> >>>> >>>> -- >>>> 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. >>>> For more options, visit https://groups.google.com/groups/opt_out. >>>> >>> >>> -- >>> 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. >>> For more options, visit https://groups.google.com/groups/opt_out. >>> >> >> -- >> 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. >> For more options, visit https://groups.google.com/groups/opt_out. >> > >

1 0

Re: large PyWavelets update, please test
by Ralf Gommers 04 Oct '13

04 Oct '13

On Fri, Oct 4, 2013 at 12:46 PM, Stuart Mumford <stuart(a)mumford.me.uk>wrote: > Hi Ralf, > > I realise the license is pants! We are making efforts to contact the > author and persuade him to change it! ;) > The original author can't do this, you also need at least permission from Torrence/Compo as well as from these guys: http://noc.ac.uk/using-science/crosswavelet-wavelet-coherence. And maybe also from A. Brazhe; can't check because the link to his site is dead. So the odds you can get the license changed seem on the low side. The reason we are looking at this is it has all the features my friend > needed, so it seemed easier (at least from a getting work done perspective) > to start with this code, which also happened to be a (far to direct) > implementation of the IDL code he was having to use before. > > While it would be nice to build some or all of this into a bigger package, > at the end of the day just having a decent Python implementation of the C. > Torrence and G. P. Compo wavelet code will be yet another thing people > don't need IDL for. > I just checked the Matlab code from http://paos.colorado.edu/research/wavelets/ (I don't speak IDL) and it's not a lot of code nor is it very complicated. What I would suggest is to contact Torrence and Compo directly to see if they're willing to change to a BSD license, and otherwise just reimplement the algorithm based on their paper. > > Stuart > > P.S. I am a solar physicist and IDL is everywhere *shudders* > :) Cheers, Ralf > > > On 4 October 2013 11:41, Ralf Gommers <ralf.gommers(a)gmail.com> wrote: > >> >> >> >> On Fri, Oct 4, 2013 at 12:32 PM, Stuart Mumford <stuart(a)mumford.me.uk>wrote: >> >>> Hello, >>> >>> On the topic of wavelet's I am involved in a very small scale effort to >>> tidy up this continuous wavelet package, with (if we can contact the >>> original author) the eventual aim of making it useful and potentially a >>> part of some larger package (scipy?). >>> >>> https://github.com/nabobalis/kPyWavelet >>> >> >> Hi Stuart, that code has a license that's incompatible with both BSD and >> GPL licenses so it's pretty much useless. The amount of code there is not >> much more than what's already in scipy.signal.wavelets, so improving the >> scipy cwt code would probably be a better idea. >> >> Ralf >> >> >> >>> >>> Stuart >>> >>> >>> On 4 October 2013 09:15, François Boulogne <fboulogne(a)sciunto.org>wrote: >>> >>>> Dear skimagers, >>>> >>>> >>>> With Ralf, we initiated a "friendly" fork of pywavelet for a future >>>> inclusion in scipy and David joined us in this work. We improved the >>>> doc, removed old-fashioned codes and we are trying now to add tests. >>>> We started this because I was considering this ticket: >>>> https://github.com/scikit-image/scikit-image/issues/602 >>>> Indeed, I believe wavelets may be useful for scikit-image. Instead of >>>> requiring a new dependency, I thought it is much more valuable to >>>> integrate the code in scipy and this is now in the workplan for >>>> scipy1.0. >>>> >>>> If some of you used pywavelet before, we would be grateful to you if you >>>> can check your code against the fork. It must be fully compatible with >>>> pywavelets. >>>> >>>> Thanks! >>>> Cheers. >>>> François. >>>> >>>> >>>> -------- Message original -------- >>>> Sujet: large PyWavelets update, please test >>>> Date : Tue, 1 Oct 2013 17:56:36 +0200 >>>> De : Ralf Gommers <ralf.gommers(a)gmail.com> >>>> Pour : pywavelets(a)googlegroups.com >>>> Copie à : François Boulogne <fboulogne(a)sciunto.org>, >>>> david.menendez.hurtado(a)scilifelab.se >>>> >>>> >>>> >>>> Hi all, >>>> >>>> https://github.com/nigma/pywt/pull/7 contains a large refactoring of >>>> PyWavelets, with contributions from Francois Boulogne, David Menendez >>>> Hurtado and myself. Main feature is support for Python 3 (single code >>>> base). Other changes are: >>>> >>>> - Numpy style docstrings for all public functions >>>> - A unit test suite with reasonable coverage (see >>>> https://coveralls.io/r/rgommers/pywt) >>>> - PEP8 and Numpy C code standard compliance >>>> - Changes to source tree layout, build setup, Numpy interfaces and C and >>>> Cython templating to more standard styles. >>>> >>>> This set of changes is supposed to be fully backwards compatible. They >>>> were quite invasive though (~150 commits), so there's a decent chance >>>> that some things not covered by the test suite were broken in the >>>> process. To catch those now, it would be very helpful if people could >>>> test their own code against either use the PR or the master branch of >>>> https://github.com/rgommers/pywt. >>>> >>>> While we've kept full backwards compatibility so far, we've also >>>> compiled a list of things that could be improved in the current API: >>>> https://github.com/rgommers/pywt/issues/38. Please add suggestions >>>> there >>>> if you have them. >>>> >>>> Cheers, >>>> 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. >>>> For more options, visit https://groups.google.com/groups/opt_out. >>>> >>> >>> -- >>> 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. >>> For more options, visit https://groups.google.com/groups/opt_out. >>> >> >> -- >> 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. >> For more options, visit https://groups.google.com/groups/opt_out. >> > > -- > 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. > For more options, visit https://groups.google.com/groups/opt_out. >

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Re: umfpack error
by Juan Nunez-Iglesias 04 Oct '13

04 Oct '13

Just for future reference, and because it wasn't immediately obvious from googling: the umfpack headers in Ubuntu 13.04 are in the package libsuitesparse-dev. But now the scipy build fails with some weird error. Hmmm. building extension "scipy.sparse.linalg.dsolve.umfpack.__umfpack" sources creating build/src.linux-x86_64-2.7/scipy/sparse/linalg/dsolve creating build/src.linux-x86_64-2.7/scipy/sparse/linalg/dsolve/umfpack adding 'scipy/sparse/linalg/dsolve/umfpack/umfpack.i' to sources. swig: scipy/sparse/linalg/dsolve/umfpack/umfpack.i swig -python -I/usr/include/suitesparse -I/usr/include/suitesparse -I/usr/include/suitesparse -o build/src.linux-x86_64-2.7/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c -outdir build/src.linux-x86_64-2.7/scipy/sparse/linalg/dsolve/umfpack scipy/sparse/linalg/dsolve/umfpack/umfpack.i unable to execute swig: No such file or directory error: command 'swig' failed with exit status 1 On Fri, Oct 4, 2013 at 2:39 PM, Juan Nunez-Iglesias <jni.soma(a)gmail.com>wrote: > Thanks Josh for the detailed response and discussion! I think you're > absolutely right that it should be suppressed if pyamg is available. And > it's probably worth getting that in before the release. Happy to tackle > this. > > Juan. > > PS: I'm mostly on OSX, with some Linux on the side. =) > > > On Fri, Oct 4, 2013 at 9:17 AM, Josh Warner <silvertrumpet999(a)gmail.com>wrote: > >> Final note - umfpack enables mode='cg' in random_walker, which is better >> than brute force but not the fastest or most efficient mode. The multi-grid >> preconditioned conjugate gradient method is: mode='cg_mg'. This is >> enabled by pyamg, which is independent of umfpack and is considerably >> easier to install and use than the method I just described. >> >> Come to think of it, we probably should suppress that warning if import >> pyamg works. It incorrectly implies the user doesn't have the fastest >> mode available. >> >> On Thursday, October 3, 2013 1:21:43 AM UTC-5, Juan Nunez-Iglesias wrote: >> >> Hi guys, >>> >>> How do I build scipy with umfpack to silence this error: >>> >>> Exception AttributeError: "'UmfpackContext' object has no attribute '_symbolic'" in <bound method UmfpackContext.__del__ of <scipy.sparse.linalg.dsolve.**umfpack.umfpack.UmfpackContext object at 0x101b62050>> ignored >>> >>> and speed up random_walker? I've just been doing a pip install scipy >>> till now. >>> >>> 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(a)googlegroups.com. >> For more options, visit https://groups.google.com/groups/opt_out. >> > >

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Re: large PyWavelets update, please test
by Stuart Mumford 04 Oct '13

04 Oct '13

Hi Ralf, I realise the license is pants! We are making efforts to contact the author and persuade him to change it! ;) The reason we are looking at this is it has all the features my friend needed, so it seemed easier (at least from a getting work done perspective) to start with this code, which also happened to be a (far to direct) implementation of the IDL code he was having to use before. While it would be nice to build some or all of this into a bigger package, at the end of the day just having a decent Python implementation of the C. Torrence and G. P. Compo wavelet code will be yet another thing people don't need IDL for. Stuart P.S. I am a solar physicist and IDL is everywhere *shudders* On 4 October 2013 11:41, Ralf Gommers <ralf.gommers(a)gmail.com> wrote: > > > > On Fri, Oct 4, 2013 at 12:32 PM, Stuart Mumford <stuart(a)mumford.me.uk>wrote: > >> Hello, >> >> On the topic of wavelet's I am involved in a very small scale effort to >> tidy up this continuous wavelet package, with (if we can contact the >> original author) the eventual aim of making it useful and potentially a >> part of some larger package (scipy?). >> >> https://github.com/nabobalis/kPyWavelet >> > > Hi Stuart, that code has a license that's incompatible with both BSD and > GPL licenses so it's pretty much useless. The amount of code there is not > much more than what's already in scipy.signal.wavelets, so improving the > scipy cwt code would probably be a better idea. > > Ralf > > > >> >> Stuart >> >> >> On 4 October 2013 09:15, François Boulogne <fboulogne(a)sciunto.org> wrote: >> >>> Dear skimagers, >>> >>> >>> With Ralf, we initiated a "friendly" fork of pywavelet for a future >>> inclusion in scipy and David joined us in this work. We improved the >>> doc, removed old-fashioned codes and we are trying now to add tests. >>> We started this because I was considering this ticket: >>> https://github.com/scikit-image/scikit-image/issues/602 >>> Indeed, I believe wavelets may be useful for scikit-image. Instead of >>> requiring a new dependency, I thought it is much more valuable to >>> integrate the code in scipy and this is now in the workplan for scipy1.0. >>> >>> If some of you used pywavelet before, we would be grateful to you if you >>> can check your code against the fork. It must be fully compatible with >>> pywavelets. >>> >>> Thanks! >>> Cheers. >>> François. >>> >>> >>> -------- Message original -------- >>> Sujet: large PyWavelets update, please test >>> Date : Tue, 1 Oct 2013 17:56:36 +0200 >>> De : Ralf Gommers <ralf.gommers(a)gmail.com> >>> Pour : pywavelets(a)googlegroups.com >>> Copie à : François Boulogne <fboulogne(a)sciunto.org>, >>> david.menendez.hurtado(a)scilifelab.se >>> >>> >>> >>> Hi all, >>> >>> https://github.com/nigma/pywt/pull/7 contains a large refactoring of >>> PyWavelets, with contributions from Francois Boulogne, David Menendez >>> Hurtado and myself. Main feature is support for Python 3 (single code >>> base). Other changes are: >>> >>> - Numpy style docstrings for all public functions >>> - A unit test suite with reasonable coverage (see >>> https://coveralls.io/r/rgommers/pywt) >>> - PEP8 and Numpy C code standard compliance >>> - Changes to source tree layout, build setup, Numpy interfaces and C and >>> Cython templating to more standard styles. >>> >>> This set of changes is supposed to be fully backwards compatible. They >>> were quite invasive though (~150 commits), so there's a decent chance >>> that some things not covered by the test suite were broken in the >>> process. To catch those now, it would be very helpful if people could >>> test their own code against either use the PR or the master branch of >>> https://github.com/rgommers/pywt. >>> >>> While we've kept full backwards compatibility so far, we've also >>> compiled a list of things that could be improved in the current API: >>> https://github.com/rgommers/pywt/issues/38. Please add suggestions there >>> if you have them. >>> >>> Cheers, >>> 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. >>> For more options, visit https://groups.google.com/groups/opt_out. >>> >> >> -- >> 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. >> For more options, visit https://groups.google.com/groups/opt_out. >> > > -- > 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. > For more options, visit https://groups.google.com/groups/opt_out. >

1 0

Re: large PyWavelets update, please test
by Ralf Gommers 04 Oct '13

04 Oct '13

On Fri, Oct 4, 2013 at 12:32 PM, Stuart Mumford <stuart(a)mumford.me.uk>wrote: > Hello, > > On the topic of wavelet's I am involved in a very small scale effort to > tidy up this continuous wavelet package, with (if we can contact the > original author) the eventual aim of making it useful and potentially a > part of some larger package (scipy?). > > https://github.com/nabobalis/kPyWavelet > Hi Stuart, that code has a license that's incompatible with both BSD and GPL licenses so it's pretty much useless. The amount of code there is not much more than what's already in scipy.signal.wavelets, so improving the scipy cwt code would probably be a better idea. Ralf > > Stuart > > > On 4 October 2013 09:15, François Boulogne <fboulogne(a)sciunto.org> wrote: > >> Dear skimagers, >> >> >> With Ralf, we initiated a "friendly" fork of pywavelet for a future >> inclusion in scipy and David joined us in this work. We improved the >> doc, removed old-fashioned codes and we are trying now to add tests. >> We started this because I was considering this ticket: >> https://github.com/scikit-image/scikit-image/issues/602 >> Indeed, I believe wavelets may be useful for scikit-image. Instead of >> requiring a new dependency, I thought it is much more valuable to >> integrate the code in scipy and this is now in the workplan for scipy1.0. >> >> If some of you used pywavelet before, we would be grateful to you if you >> can check your code against the fork. It must be fully compatible with >> pywavelets. >> >> Thanks! >> Cheers. >> François. >> >> >> -------- Message original -------- >> Sujet: large PyWavelets update, please test >> Date : Tue, 1 Oct 2013 17:56:36 +0200 >> De : Ralf Gommers <ralf.gommers(a)gmail.com> >> Pour : pywavelets(a)googlegroups.com >> Copie à : François Boulogne <fboulogne(a)sciunto.org>, >> david.menendez.hurtado(a)scilifelab.se >> >> >> >> Hi all, >> >> https://github.com/nigma/pywt/pull/7 contains a large refactoring of >> PyWavelets, with contributions from Francois Boulogne, David Menendez >> Hurtado and myself. Main feature is support for Python 3 (single code >> base). Other changes are: >> >> - Numpy style docstrings for all public functions >> - A unit test suite with reasonable coverage (see >> https://coveralls.io/r/rgommers/pywt) >> - PEP8 and Numpy C code standard compliance >> - Changes to source tree layout, build setup, Numpy interfaces and C and >> Cython templating to more standard styles. >> >> This set of changes is supposed to be fully backwards compatible. They >> were quite invasive though (~150 commits), so there's a decent chance >> that some things not covered by the test suite were broken in the >> process. To catch those now, it would be very helpful if people could >> test their own code against either use the PR or the master branch of >> https://github.com/rgommers/pywt. >> >> While we've kept full backwards compatibility so far, we've also >> compiled a list of things that could be improved in the current API: >> https://github.com/rgommers/pywt/issues/38. Please add suggestions there >> if you have them. >> >> Cheers, >> 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. >> For more options, visit https://groups.google.com/groups/opt_out. >> > > -- > 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. > For more options, visit https://groups.google.com/groups/opt_out. >

1 0

Fwd: large PyWavelets update, please test
by François Boulogne 04 Oct '13

04 Oct '13

Dear skimagers, With Ralf, we initiated a "friendly" fork of pywavelet for a future inclusion in scipy and David joined us in this work. We improved the doc, removed old-fashioned codes and we are trying now to add tests. We started this because I was considering this ticket: https://github.com/scikit-image/scikit-image/issues/602 Indeed, I believe wavelets may be useful for scikit-image. Instead of requiring a new dependency, I thought it is much more valuable to integrate the code in scipy and this is now in the workplan for scipy1.0. If some of you used pywavelet before, we would be grateful to you if you can check your code against the fork. It must be fully compatible with pywavelets. Thanks! Cheers. François. -------- Message original -------- Sujet: large PyWavelets update, please test Date : Tue, 1 Oct 2013 17:56:36 +0200 De : Ralf Gommers <ralf.gommers(a)gmail.com> Pour : pywavelets(a)googlegroups.com Copie à : François Boulogne <fboulogne(a)sciunto.org>, david.menendez.hurtado(a)scilifelab.se Hi all, https://github.com/nigma/pywt/pull/7 contains a large refactoring of PyWavelets, with contributions from Francois Boulogne, David Menendez Hurtado and myself. Main feature is support for Python 3 (single code base). Other changes are: - Numpy style docstrings for all public functions - A unit test suite with reasonable coverage (see https://coveralls.io/r/rgommers/pywt) - PEP8 and Numpy C code standard compliance - Changes to source tree layout, build setup, Numpy interfaces and C and Cython templating to more standard styles. This set of changes is supposed to be fully backwards compatible. They were quite invasive though (~150 commits), so there's a decent chance that some things not covered by the test suite were broken in the process. To catch those now, it would be very helpful if people could test their own code against either use the PR or the master branch of https://github.com/rgommers/pywt. While we've kept full backwards compatibility so far, we've also compiled a list of things that could be improved in the current API: https://github.com/rgommers/pywt/issues/38. Please add suggestions there if you have them. Cheers, Ralf

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scikit-image October 2013