Hi Troels, I'll also now stop making changes to your branch. If you need anything else, just say. Note that the state.load user function is much slower than state.save. I'm not sure why that is. But a little bit of time can be saved if you don't compress the state files (compress_type=0).
Regards, Edward On 8 December 2014 at 18:02, Edward d'Auvergne <edw...@nmr-relax.com> wrote: > I've updated most of the system tests. However there are two that > show that the software verification tests will fail. For example: > > ====================================================================== > ERROR: test_plot_contour_cpmg (test_suite.system_tests.nmrglue.Nmrglue) > Test the plot_contour function in pipe_control. > ---------------------------------------------------------------------- > > relax> pipe.create(pipe_name='mf', pipe_type='mf', bundle=None) > > relax> spectrum.nmrglue_read(file='128_0_FT.ft2', > dir='/data/relax/branches/nmrglue/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data', > nmrglue_id='128_0_FT') > Traceback (most recent call last): > File "/data/relax/branches/nmrglue/test_suite/system_tests/nmrglue.py", > line 441, in test_plot_contour_cpmg > self.setup_plot_contour_cpmg(show=False) > File "/data/relax/branches/nmrglue/test_suite/system_tests/nmrglue.py", > line 192, in setup_plot_contour_cpmg > ax = plot_contour(nmrglue_id=sp_id, contour_start=200000., > contour_num=20, contour_factor=1.20, ppm=True, show=show) > File "/data/relax/branches/nmrglue/pipe_control/nmrglue.py", line > 158, in plot_contour > ax = contour_plot(nmrglue_id=nmrglue_id, > contour_start=contour_start, contour_num=contour_num, > contour_factor=contour_factor, ppm=ppm, show=show) > File "/data/relax/branches/nmrglue/lib/software/nmrglue.py", line > 59, in contour_plot > dic = cdp.nmrglue_dic[nmrglue_id] > AttributeError: 'PipeContainer' object has no attribute 'nmrglue_dic' > > ---------------------------------------------------------------------- > > Here the lib.software.nmrglue module is not allowed to access the > relax data store, as it must be independent of it. Instead, simply > pass in the dic, udic and data nmrglue objects from the data store > when needed. > > Regards, > > Edward > > > > > > On 8 December 2014 at 17:53, Edward d'Auvergne <edw...@nmr-relax.com> wrote: >> 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
