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 <[email protected]>: > 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 <[email protected]> > 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 <[email protected]> > 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 >
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