large PyWavelets update, please test

Fri Oct 4 08:22:48 EDT 2013

On Fri, Oct 4, 2013 at 1:56 PM, Stuart Mumford <stuart at 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 at gmail.com> wrote:
>
>>
>>
>>
>> On Fri, Oct 4, 2013 at 1:04 PM, Ralf Gommers <ralf.gommers at gmail.com>wrote:
>>
>>>
>>>
>>>
>>> On Fri, Oct 4, 2013 at 12:46 PM, Stuart Mumford <stuart at 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 at gmail.com> wrote:
>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Fri, Oct 4, 2013 at 12:32 PM, Stuart Mumford <stuart at 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 at 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 at gmail.com>
>>>>>>> Pour :  pywavelets at googlegroups.com
>>>>>>> Copie à :       François Boulogne <fboulogne at sciunto.org>,
>>>>>>> david.menendez.hurtado at 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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