Hmmm, I don't think it's related. Maybe it is time to unify 'ri_data', at least between the model-free analysis and relaxation dispersion. This might be the best solution for handling fixed and optimised R1 values as the same thing (as well as optimised R2/R1rho values).
The 'ri_data' concept is the key behind the relax_data user functions. The relax_data.read user function is used to read in R1 data and store it in 'ri_data', so maybe we should use this for the optimised values as well. This would of course include the R2 parameter as well. The values are then written out with the relax_data.write user function. For the grace.write function, the relevant key needs to be supplied to obtain the correct values. Note that the current relaxation data design creates a number of data structures. In the base data pipe 'cdp', it creates the cdp.ri_ids list and cdp.ri_type dictionary, and stores the spectrometer frequency in a dictionary. For the spins it creates the ri_data and ri_data_err dictionaries which contain the values and errors. So you would need to create a key for each R1 data set per experiment and field strength (it is offset, spin, and dispersion point independent), store the key, data type, and frequency in cdp, and store the values and errors in the spin containers. See the pipe_control.relax_data.pack_data() function, as that will do it automatically for you: http://www.nmr-relax.com/api/3.2/pipe_control.relax_data-module.html#pack_data http://www.nmr-relax.com/api/3.2/pipe_control.relax_data-pysrc.html#pack_data I think that using this approach will solve all of the strange problems. And is will allow you to use the relax_data user functions so you can access a lot of already implemented infrastructure. If you are interested in this clean solution, I would suggest that you copy the 'r1' and 'r2' parameter object definition into the base class into a new _add_ri_data() method, as is done for the other analysis independent parameters, and merge the two into one 'ri_data' parameter. Then use the pack_data() function to store data. You also have access to the create_frq_label(), delete(), return_value(), and write() functions. You could then replace calls to the value.write user function with relax_data.write. The grace.write user function should work without changes, if you pass in the correct key. Regards, Edward On 19 August 2014 16:54, Troels Emtekær Linnet <[email protected]> wrote: > Hi Edward. > > Well, it seemed that my problems was fixed. > > I haven't met any problems since then. > > There was though an issue, with the test script you just provided. > > I could not find any values in the: 'r1rho_prime.out' file. > > If I add: 'TP02 R1 fit' to the model list, I get r1.out to also be empty. > > I wonder if that was my fix to: > https://gna.org/support/index.php?3121 > > Best > Troels > > 2014-08-19 16:36 GMT+02:00 Edward d'Auvergne <[email protected]>: >> Hi, >> >> This is a difficult problem as R1 values are normally stored in the >> ri_data dictionary object, the same place that R2 values are stored. >> I don't have an easy solution for this, but future attempts at >> unifying the handling of relaxation data in all analyses will affect >> your current work. For example the 'r1' parameter here will probably >> be converted into 'ri_data', and the 'ri_data' object set up with a >> special method in the base Parameter_object class. The 'ri_data' >> object is correctly handled by value.set and grace.write, but the >> current implementation in the model-free parameter object is ugly. >> Does your implementation now work correctly? >> >> Regards, >> >> Edward >> >> >> >> On 15 August 2014 18:54, <[email protected]> wrote: >>> Author: tlinnet >>> Date: Fri Aug 15 18:54:01 2014 >>> New Revision: 25036 >>> >>> URL: http://svn.gna.org/viewcvs/relax?rev=25036&view=rev >>> Log: >>> Fix in relax_disp API, how to handle the r1_fit parameter type. >>> >>> bug #22470(https://gna.org/bugs/index.php?22470): value.set does not work >>> for parameter r1_fit. >>> >>> Modified: >>> trunk/specific_analyses/relax_disp/api.py >>> >>> Modified: trunk/specific_analyses/relax_disp/api.py >>> URL: >>> http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/api.py?rev=25036&r1=25035&r2=25036&view=diff >>> ============================================================================== >>> --- trunk/specific_analyses/relax_disp/api.py (original) >>> +++ trunk/specific_analyses/relax_disp/api.py Fri Aug 15 18:54:01 2014 >>> @@ -1001,8 +1001,29 @@ >>> if error: >>> obj_name += '_err' >>> >>> + # Handle the R10 parameters. >>> + if param[i] in ['r1_fit']: >>> + # Loop over the current keys. >>> + for exp_type, frq, ei, mi in >>> loop_exp_frq(return_indices=True): >>> + # The parameter key. >>> + key = generate_r20_key(exp_type=exp_type, frq=frq) >>> + >>> + # Initialise the structure if needed. >>> + if not hasattr(spin, obj_name): >>> + setattr(spin, obj_name, {}) >>> + >>> + # Set the value. >>> + if index == None: >>> + obj = getattr(spin, obj_name) >>> + obj[key] = value[i] >>> + >>> + # If the index is specified, let it match the >>> frequency index >>> + elif mi == index: >>> + obj = getattr(spin, obj_name) >>> + obj[key] = value[i] >>> + >>> # Handle the R20 parameters. >>> - if param[i] in PARAMS_R20: >>> + elif param[i] in PARAMS_R20: >>> # Loop over the current keys. >>> for exp_type, frq, ei, mi in >>> loop_exp_frq(return_indices=True): >>> # The parameter key. >>> >>> >>> _______________________________________________ >>> relax (http://www.nmr-relax.com) >>> >>> This is the relax-commits mailing list >>> [email protected] >>> >>> 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-commits >> >> _______________________________________________ >> relax (http://www.nmr-relax.com) >> >> This is the relax-devel mailing list >> [email protected] >> >> 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 _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] 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
