:) I'm looking through the functions of the disp_data module and have found one other place where the offset should be supported - the loop_spectrum_ids() function. As the test suite now passes, it might be a good idea to create a quick unit test for each function you change. This is just to be certain that each function is functioning as you would expect. Using your CPMG and R1rho data saved states, the function could be tested on both to make sure that all data types operate correctly.
Note that in the future, relax many support offset effects in the CPMG as well. This is currently the major benefit of using Flemming Hansen's CATIA software. Such support would be quite easy to add, as relax already handles the offset concept for R1rho data and the use of R1 data. It would simply require a new user function for inputting hard pulse information and a new numeric model which uses the correct matrices. This information is just for future reference, there is no need for an implementation at the moment. Therefore this is listed in the TODO section of the dispersion chapter in the manual (http://www.nmr-relax.com/manual/do_dispersion_features_yet_be_implemented.html) Cheers, Edward On 27 February 2014 12:40, Troels Emtekær Linnet <tlin...@nmr-relax.com> wrote: > That sounds perfect. :-) > > And I say, that I now know what to do after Lunch. > > Never gonna give "it" up... never gonna... > https://www.youtube.com/watch?v=dQw4w9WgXcQ > > Best > Troels > > > > > 2014-02-27 12:37 GMT+01:00 Edward d'Auvergne <edward.dauver...@gmail.com>: > >> Actually, by grepping the source code: >> >> $ grep "find_intensity_keys([a-z]" -r . --exclude-dir=.svn >> >> I can see many places where find_intensity_keys() is incorrectly >> called! I think it's obvious that this function came before >> R1rho-type data was supported. Looking further, the >> return_intensity() function is also deficient for the offset value! >> Almost everywhere where find_intensity_keys() is called is incorrectly >> implemented (excluding the specific_analyses.relax_disp.nessy module >> as NESSY does not support R1rho data)! These should all be fixed >> otherwise problems will appear in your analysis later on. >> >> Thinking about the problem even more, I can see that only one key is >> ever used when calling find_intensity_keys(). The purpose of having a >> list of keys has been permanently lost - I remember implementing this >> as a feature earlier in the relax_disp branch development but the >> reason for it no longer exists. As a clean solution, I would suggest: >> >> - Renaming the function to find_intensity_key() and have it return a >> single value. >> - Have the find_intensity_key() function raise a RelaxError if more >> than one key is found. >> - Modify all of the code calling find_intensity_key() to expect and >> handle a single key. >> - Modify the return_intensity() function to be more like the >> average_intensity() function in that the offset argument is supported. >> >> This solution would be much more maintainable in the future. What do you >> think? >> >> Regards, >> >> Edward >> >> On 27 February 2014 12:08, Edward d'Auvergne <edward.dauver...@gmail.com> >> wrote: >> > Hi, >> > >> > This looks like another rather stupid typo/mistake :) I added a print >> > statement for the int_keys variable and ran the test. There should >> > only be one key for a given {exp_type, frq, offset, point, time} >> > metadata set, but the printout shows this not to be the case. If you >> > carefully look at the find_intensity_keys() call, you will see that >> > one of these 5 bits of information are not sent in as an argument ;) >> > >> > Regards, >> > >> > Edward >> > >> > >> > >> > >> > On 27 February 2014 11:38, Troels Emtekær Linnet <tlin...@nmr-relax.com> >> > wrote: >> >> Hi Edward. >> >> >> >> When I run: >> >> ./relax -s >> >> Relax_disp.test_bug_21344_sparse_time_spinlock_acquired_r1rho_fail_relax_disp >> >> >> >> I get: >> >> ------------------- >> >> Parameter values: [2.4392597217423719, 149801.17120634759] >> >> Function value: 252.36349493927844 >> >> Iterations: 135 >> >> Function calls: 281 >> >> Gradient calls: 0 >> >> Hessian calls: 0 >> >> Warning: None >> >> >> >> >> >> relax> eliminate(function=None, args=None) >> >> >> >> relax> monte_carlo.setup(number=5) >> >> >> >> relax> monte_carlo.create_data(method='back_calc') >> >> Traceback (most recent call last): >> >> File >> >> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/test_suite/system_tests/relax_disp.py", >> >> line 284, in >> >> test_bug_21344_sparse_time_spinlock_acquired_r1rho_fail_relax_disp >> >> relax_disp.Relax_disp(pipe_name='base pipe', >> >> pipe_bundle='relax_disp', results_dir=self.tmpdir, models=['R2eff'], >> >> grid_inc=3, mc_sim_num=5, modsel='AIC', pre_run_dir=None, >> >> insignificance=1.0, numeric_only=False, mc_sim_all_models=False, >> >> eliminate=True) >> >> File >> >> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/auto_analyses/relax_disp.py", >> >> line 118, in __init__ >> >> self.run() >> >> File >> >> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/auto_analyses/relax_disp.py", >> >> line 471, in run >> >> self.optimise(model=model) >> >> File >> >> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/auto_analyses/relax_disp.py", >> >> line 379, in optimise >> >> self.interpreter.monte_carlo.create_data() >> >> File >> >> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/prompt/uf_objects.py", >> >> line 221, in __call__ >> >> self._backend(*new_args, **uf_kargs) >> >> File >> >> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/pipe_control/monte_carlo.py", >> >> line 113, in create_data >> >> pack_sim_data(data_index, random) >> >> File >> >> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/specific_analyses/relax_disp/api.py", >> >> line 1609, in sim_pack_data >> >> raise RelaxError("Monte Carlo simulation data for the key '%s' >> >> already exists." % int_key) >> >> RelaxError: RelaxError: Monte Carlo simulation data for the key >> >> '1_0_46_0' already exists. >> >> >> >> --------------------- >> >> >> >> I have looked into: >> >> specific_analyses/relax_disp/api.py >> >> >> >> There it is: >> >> ---------------------------------------------- >> >> def sim_pack_data(self, data_id, sim_data): >> >> """Pack the Monte Carlo simulation data. >> >> >> >> @param data_id: The tuple of the spin container and the >> >> exponential curve identifying key, as yielded by the base_data_loop() >> >> generator method. >> >> @type data_id: SpinContainer instance and float >> >> @param sim_data: The Monte Carlo simulation data. >> >> @type sim_data: list of float >> >> """ >> >> >> >> # The R2eff model (with peak intensity base data). >> >> if cdp.model_type == 'R2eff': >> >> # Unpack the data. >> >> spin, exp_type, frq, offset, point = data_id >> >> >> >> # Initialise the data structure if needed. >> >> if not hasattr(spin, 'intensity_sim'): >> >> spin.intensity_sim = {} >> >> >> >> # Loop over each time point. >> >> ti = 0 >> >> for time in loop_time(exp_type=exp_type, frq=frq, >> >> offset=offset, point=point): >> >> # Get the intensity keys. >> >> int_keys = find_intensity_keys(exp_type=exp_type, >> >> frq=frq, point=point, time=time) >> >> >> >> # Loop over the intensity keys. >> >> for int_key in int_keys: >> >> # Test if the simulation data point already exists. >> >> if int_key in spin.intensity_sim: >> >> raise RelaxError("Monte Carlo simulation data >> >> for the key '%s' already exists." % int_key) >> >> >> >> # Initialise the list. >> >> spin.intensity_sim[int_key] = [] >> >> >> >> # Loop over the simulations, appending the >> >> corresponding data. >> >> for i in range(cdp.sim_number): >> >> >> >> spin.intensity_sim[int_key].append(sim_data[i][ti]) >> >> >> >> # Increment the time index. >> >> ti += 1 >> >> --------------------- >> >> >> >> For me, this looks okay. >> >> >> >> Do you have an Idea why this is not working? >> >> >> >> Best >> >> Troels > > _______________________________________________ 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
