Re: Implement handles for nmrglue in relax -- December 02, 2014 - 17:41

I uploaded the nmrglue logo in a number of formats including a SVG and 
PS from which high-res raster images can be created to 
https://github.com/jjhelmus/nmrglue_logo.  Feel free to include these or 
files generated from these in relax.

    - Jonathan Helmus

On 12/01/2014 12:37 PM, Jonathan Helmus wrote:
> Edward and Troels,
>
>     A few points regarding nmrglue in this discussion.  The main 
> nmrglue website is www.nmrglue.com, links to that site are best in any 
> documentation or credits.  The source code and issue tracker are on 
> GitHub at https://github.com/jjhelmus/nmrglue.
>
>     The representation of NMR data is in NumPy multi-dimenstional 
> ndarray objects [1].  These can be serialized to strings using the 
> .tostring() or .tobytes() methods.  Spectral metadata is stored in a 
> Python dictionary, there are a number of options for serializing 
> these.  Also both objects can be pickled.
>
>     Python 3 support is available in the development version of 
> nmrglue, 0.5-dev, available on GitHub.  There is an issue with 
> installing the package in a Python 3 environment which I need to work 
> out but then I plan or releasing version 0.5 which will be the first 
> release to support Python 3.  Expect it out and available on PyPI by 
> the end of the week.
>
>     I have an SVG file of the nmrglue logo from which the small jpg 
> was created.  I'll need to find where it is stored on my computer at 
> home but I'll send it along with a higher resolution png/jpg once I 
> locate it.
>
>     Best of luck on getting relax to play nicely with nmrglue.  If 
> there is anything I can do to help on the nmrglue side feel free to 
> ask.  nmrglue is BSD licensed and I would like to keep it that way, if 
> you send any code my way I'd appreciate if it could be licensed under 
> the same terms.
>
> Cheers,
>
>     - Jonathan Helmus
>
>
> [1] 
> http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html
>
> On 11/27/2014 07:30 AM, Edward d'Auvergne wrote:
> > Hi Troels,
> >
> > This appears to be the main nmrglue website http://www.nmrglue.com/ .
> > I can see here that there is an nmrglue icon
> > (http://www.nmrglue.com/images/nmrglue_logo.jpg).  This may be useful
> > for the relax GUI graphics for the spectrum.nmrglue_* user function
> > menu entries and wizard pages.  The wizard graphics (in the
> > graphics/wizard directory) have a width of 200 px though.  You should
> > ask on the nmrglue forum
> > (http://groups.google.com/group/nmrglue-discuss) about the use of such
> > a graphic and if there is a higher resolution version.
> >
> > Cheers,
> >
> > Edward
> >
> > On 27 November 2014 at 12:16, Edward d'Auvergne 
> > <edward@xxxxxxxxxxxxx> wrote:
> > > Hi,
> > >
> > > This sounds good.  And rather simple, the backend of the
> > > spectrum.nmrglue_read user function could simply be the single line of
> > > the tutorial 
> > > http://nmrglue.readthedocs.org/en/latest/tutorial.html#reading-nmr-files:
> > >
> > > > > > import nmrglue as ng
> > > > > > dic,data = ng.pipe.read("test.fid")
> > > For the *.ft2 files, how big are they?  I wonder if you can downsample
> > > the original *.fid files so that the *.ft2 files are within 10 to 100
> > > kB (using the nmrPipe extract command, etc.).  Anyway, just add a
> > > system test, and we can then discuss more of the design before
> > > implementing the nmrglue interface.  From your aims, it sounds pretty
> > > straightforward.  If the number of relax spectrum.nmrglue_* user
> > > functions expand significantly to access more of the nmrglue
> > > functionality, maybe we can create a dedicated nmrglue user function
> > > class later on.  Anyway, we just have to make sure that relax
> > > continues to operate smoothly when the scipy/matplotlib/nmrglue
> > > packages are absent.
> > >
> > > One problem will be storage of the nmrglue data.  This will probably
> > > not fit into the relax data store, as it absolutely requires to_xml()
> > > and from_xml() methods to allow the data to be saved and read again.
> > > Any ideas?  We could create a special class in lib.spectrum.nmrglue
> > > which uses the singleton design pattern
> > > (https://en.wikipedia.org/wiki/Singleton_pattern), as is used
> > > extensively in relax.  Just 'grep -i' for 'singleton'.  The data
> > > storage would then be temporary.  Or, ideally, we could modify the
> > > nmrglue data structures to be convertible to and from XML. Some ideas
> > > should be discussed with the nmrglue authors though (which is why I
> > > have CCed Jonathan, so he knows we are developing a simple
> > > relax-nmrglue interface).  At the moment, I don't know much about the
> > > nmrglue designs.
> > >
> > > For the user functions, do you know if nmrglue has an icon that we can
> > > use for the menus and user function wizard pages in the GUI?
> > >
> > > Cheers,
> > >
> > > Edward
> > >
> > >
> > >
> > > On 27 November 2014 at 11:54, Troels Emtekær Linnet 
> > > <tlinnet@xxxxxxxxx> wrote:
> > > > Hi Edward.
> > > >
> > > > To:
> > > > test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060521/cpmg_disp_sod1d90a_060521_normal.fid/ft2_data 
> > > >
> > > >
> > > > I will add the corresponding .ft2 files. To limit size use, I will 
> > > > add just
> > > > very few .ft2 files.
> > > >
> > > > I will add wrapper functions which will:
> > > > - read a ft2 file
> > > > - read a range of ft2 files according to a glob of file names
> > > > - plot the spectrum
> > > >
> > > > manipulate the numpy arrray, to certain functions.
> > > >
> > > > Plotting in matplotlib.
> > > >
> > > > Best
> > > > Troels
> > > >
> > > >
> > > >
> > > >
> > > > Troels Emtekær Linnet
> > > >
> > > > 2014-11-27 11:33 GMT+01:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> > > > > Hi Troels,
> > > > >
> > > > > This is no problem.  Just create the branch.  But before adding code,
> > > > > we should discuss the design.  This has two benefits - it will be 
> > > > > much
> > > > > simpler for you in the long run, and it would avoid any redesigns if
> > > > > the first attempt doesn't fit into the relax infrastructure well.
> > > > > Could you describe nmrglue, including links, and what you'd like 
> > > > > to do
> > > > > with it?  Would you like to interact with the program at runtime, or
> > > > > simply read its output?  Would you like to create input files?
> > > > >
> > > > > Cheers,
> > > > >
> > > > > Edward
> > > > >
> > > > >
> > > > >
> > > > > On 27 November 2014 at 11:01, Troels Emtekær Linnet 
> > > > > <tlinnet@xxxxxxxxx>
> > > > > wrote:
> > > > > > Dear Edward.
> > > > > >
> > > > > > I am about to setup a new test branch for using nmrglue.
> > > > > >
> > > > > > I would need to compare all intensities in a long range of spectra.
> > > > > >
> > > > > > I will setup a new branch by:
> > > > > > http://wiki.nmr-relax.com/Git_branch_creation
> > > > > >
> > > > > > I already have some test code, which is working.
> > > > > >
> > > > > > I am a little unsure where this will be going.
> > > > > >
> > > > > > But essentially, I would like to write some wrapper functions to
> > > > > > nmrglue,
> > > > > > which can be handsome.
> > > > > >
> > > > > > Best
> > > > > > Troels Emtekær Linnet
> > > > > > _______________________________________________
> > > > > > relax (http://www.nmr-relax.com)
> > > > > >
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