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 _______________________________________________ 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
