Hi Troels, It's all done. It took a while longer than I though. That was my fault, as I made the nmrglue objects of the relax data store a lot more flexible. Hence the commit is far more complicated than actually required (http://article.gmane.org/gmane.science.nmr.relax.scm/24773). You now have:
cdp.nmrglue -> data_store.nmrglue.Nmrglue_dict dictionary instance (it inherits from data_store.data_classes.RelaxDictType). cdp.nmrglue[key] -> data_store.nmrglue.Nmrglue instance (it inherits from data_store.data_classes.Element). cdp.nmrglue[key].dic -> the nmrglue dic object. cdp.nmrglue[key].udic -> the nmrglue udic object. cdp.nmrglue[key].data -> the nmrglue numpy.float32 data object. The Nmrglue.test_save_state system test now passes. Have a look at a relax save file for what is now being created. Regards, Edward On 8 December 2014 at 15:39, Edward d'Auvergne <edw...@nmr-relax.com> wrote: > Ok, so I'll start moving things around in your branch. > > Regards, > > Edward > > On 8 December 2014 at 15:37, Troels Emtekær Linnet > <tlin...@nmr-relax.com> wrote: >> That sound good ! >> >> 2014-12-08 15:34 GMT+01:00 Edward d'Auvergne <edw...@nmr-relax.com>: >>> >>> Hi, >>> >>> I wouldn't bother with the matplotlib data storage. If you like, I >>> could give this 10 minutes of work on the nmrglue branch and have the >>> Base64 string in XML storage fixed. The system test is in place >>> already to implement this, and I know exactly what needs to be done, >>> so it won't take long. Then we can keep the numpy format as is. I'd >>> probably restore some of your original ideas and have all data in >>> cdp.nmrglue_data which a dictionary with >>> data_store.data_classes.Element instances as its elements, and then >>> write to_xml() and from_xml() methods to handle the numpy data as >>> Base64 and all other structures are passed to the Element base class >>> methods. >>> >>> Regards, >>> >>> Edward >>> >>> >>> >>> >>> On 8 December 2014 at 15:19, Troels Emtekær Linnet >>> <tlin...@nmr-relax.com> wrote: >>> > Hi Edward. >>> > >>> > I am trying to look at my data now with the plots I have in my mind. >>> > >>> > The branch is actually in a state where I can use it. >>> > >>> > The only trouble I have, is the storing of the numpy array. >>> > >>> > I am actually not planning on saving the state, but will continuously >>> > just >>> > read from the original file. >>> > But since the numpy array is saved in cdp, to get access, then storing >>> > the >>> > state should be possible. >>> > >>> > All plots will just be made with matplotlib after the shuffling around >>> > with >>> > the numpy array. >>> > >>> > Best >>> > Troels >>> > >>> > >>> > >>> > 2014-12-08 15:14 GMT+01:00 Edward d'Auvergne <edw...@nmr-relax.com>: >>> >> >>> >> Hi Troels, >>> >> >>> >> > I think I will have to leave the implementation in relax. >>> >> >>> >> Would it take much to get the branch in a reasonable state for merging >>> >> back? Even if not everything is implemented? Well, apart from >>> >> bringing in nmrglue 0.5 when that is released. I'm sure that in the >>> >> future some PhD student or postdoc will appreciate and take up what >>> >> you have already done and expand on it. You've already put a lot of >>> >> polish on this, so it'd be a pity to not merge it. >>> >> >>> >> >>> >> > Time goes away from pursuing the analysis, and goes into rather >>> >> > annoying >>> >> > stuff. >>> >> >>> >> With coding, it's a bit hard to know what will be quick and what will >>> >> take a lot of time. It's a problem I have too. >>> >> >>> >> >>> >> > The idea is simple. >>> >> > Load one or two spectrum. >>> >> > Plot the contour, or histogram. >>> >> > Or make a correlation plot of the two spectra. >>> >> > >>> >> > Store the data. >>> >> >>> >> Storing the data in any other format always takes more effort when >>> >> combining data from different sources/software. But this is pretty >>> >> much sorted out for the nmrglue data. You could even store the >>> >> nmrglue data in the relax data store as a Base64 string and a new >>> >> variable for the ndarray shape, as a shortcut. >>> >> >>> >> >>> >> > Storing the axis plots is a different question. >>> >> > >>> >> > >>> >> > http://stackoverflow.com/questions/7290370/store-and-reload-matplotlib-pyplot-object >>> >> > >>> >> > I cannot actually do it at the moment. >>> >> > So essentially, it just storing a numpy array >>> >> >>> >> For matplotlib data, I don't think that storing these data structures >>> >> will ever be possible to implement in a compatible way. The reason is >>> >> because matplotlib is too much of a moving target. They do not have a >>> >> stable API! So I would never recommend that you tackle such a problem >>> >> in this way. That's just asking for pain ;) >>> >> >>> >> There is a much better alternative which would be more compatible with >>> >> future matplotlib versions. And that is that all the information >>> >> required to create the matplotlib plot is stored in a pure >>> >> data_store.data_classes.Element class container as simple variables >>> >> (str, bool, int, float, or a list, tuple or dict of these). This is >>> >> similar to the GUI setting storage. Then there could be a user >>> >> function to recreate the plot using the currently stored settings. >>> >> This would work much better. And it would be orders of magnitude >>> >> quicker to implement than working with matplotlib data structures. >>> >> >>> >> Regards, >>> >> >>> >> Edward >>> > >>> > >> >> _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list relax-devel@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
