Hi Edward. Do you have a feeling for how much modification of relax is needed?
There is a dependency check, that the length of cdp.relax_time_list is not larger than 1. Is it within range to allow more than one delay time? Best Troels 2014-02-18 14:21 GMT+01:00 Edward d'Auvergne <[email protected]>: > Hi Troels, > > I would then recommend you create 2 tests, as it looks to me like the > fundamental issues are the same - that the detection of 2-point verses > full exponential curves is not functioning correctly. The two tests, > once the bug is fixed, will the make sure that both these errors will > never again be seen by relax users! > > Cheers, > > Edward > > > > On 18 February 2014 12:40, Troels Emtekær Linnet <[email protected]> > wrote: >> If the systemtest is modified to: >> >> self.interpreter.calc(verbosity=1) >> >> The error is: >> >> Traceback (most recent call last): >> File >> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/test_suite/system_tests/relax_disp.py", >> line 278, in test_bug_21665_cpmg_two_fields_two_delaytimes_fail >> self.interpreter.calc(verbosity=1) >> 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/minimise.py", >> line 86, in calc >> calculate(verbosity=verbosity) >> File >> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/specific_analyses/relax_disp/api.py", >> line 717, in calculate >> self._calculate_r2eff() >> File >> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/specific_analyses/relax_disp/api.py", >> line 182, in _calculate_r2eff >> check_exp_type_fixed_time() >> File >> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/specific_analyses/relax_disp/checks.py", >> line 112, in check_exp_type_fixed_time >> raise RelaxError("The experiment '%s' is not of the fixed >> relaxation time period data type." % exp_type) >> RelaxError: RelaxError: The experiment 'SQ CPMG' is not of the fixed >> relaxation time period data type. >> >> >> 2014-02-18 12:24 GMT+01:00 Troels Emtekær Linnet <[email protected]>: >>> Hi Edward. >>> >>> The systemtest is now implemented. >>> I think this bug is related to: >>> bug #21344 (https://gna.org/bugs/?21344): Handling of in sparse >>> acquired R1rho dataset with missing combinations of time and spin-lock >>> field strengths. >>> >>> The output of the systemtest gives: >>> ------------ >>> Fitting to spin :2@N, frequency 499862140.0 and dispersion point 50.0 >>> --------------------------------------------------------------------- >>> >>> Unconstrained grid search size: 9 (constraints may decrease this size). >>> >>> Traceback (most recent call last): >>> File >>> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/test_suite/system_tests/relax_disp.py", >>> line 281, in test_bug_21665_cpmg_two_fields_two_delaytimes_fail >>> relax_disp.Relax_disp(pipe_name="compare_128_FT_R2eff", >>> pipe_bundle="cpmg_disp_sod1d90a", 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 116, in __init__ >>> self.run() >>> File >>> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/auto_analyses/relax_disp.py", >>> line 451, in run >>> self.optimise(model=model) >>> File >>> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/auto_analyses/relax_disp.py", >>> line 350, in optimise >>> self.interpreter.grid_search(inc=self.grid_inc) >>> 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/minimise.py", >>> line 152, in grid_search >>> grid_search(lower=lower, upper=upper, inc=inc, >>> constraints=constraints, verbosity=verbosity) >>> File >>> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/specific_analyses/relax_disp/api.py", >>> line 1093, in grid_search >>> self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc, >>> constraints=constraints, verbosity=verbosity, sim_index=sim_index) >>> File >>> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/specific_analyses/relax_disp/api.py", >>> line 1142, in minimise >>> self._minimise_r2eff(min_algor=min_algor, min_options=min_options, >>> func_tol=func_tol, grad_tol=grad_tol, max_iterations=max_iterations, >>> constraints=constraints, scaling=scaling, verbosity=verbosity, >>> sim_index=sim_index, lower=lower, upper=upper, inc=inc) >>> File >>> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/specific_analyses/relax_disp/api.py", >>> line 382, in _minimise_r2eff >>> values.append(average_intensity(spin=spin, exp_type=exp_type, >>> frq=frq, offset=offset, point=point, time=time, sim_index=sim_index)) >>> File >>> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/specific_analyses/relax_disp/disp_data.py", >>> line 114, in average_intensity >>> int_keys = find_intensity_keys(exp_type=exp_type, frq=frq, >>> offset=offset, point=point, time=time) >>> File >>> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/specific_analyses/relax_disp/disp_data.py", >>> line 347, in find_intensity_keys >>> raise RelaxError("No intensity data could be found corresponding >>> to the spectrometer frequency of %s MHz, dispersion point of %s and >>> relaxation time of %s s." % (frq*1e-6, point, time)) >>> RelaxError: RelaxError: No intensity data could be found corresponding >>> to the spectrometer frequency of 499.86214 MHz, dispersion point of >>> 50.0 and relaxation time of 0.06 s. >>> >>> ----------------------------- >>> >>> This is true. >>> For the relaxation time of 0.06 s, there is no dispersion point of 50.0. >>> >>> Best >>> Troels >>> >>> 2014-02-18 12:19 GMT+01:00 <[email protected]>: >>>> Author: tlinnet >>>> Date: Tue Feb 18 12:19:41 2014 >>>> New Revision: 22198 >>>> >>>> URL: http://svn.gna.org/viewcvs/relax?rev=22198&view=rev >>>> Log: >>>> Added systemtest to catch bug: relax -s >>>> Relax_disp.test_bug_21665_cpmg_two_fields_two_delaytimes_fail >>>> >>>> Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG >>>> analysis with two fields at two delay times. >>>> >>>> Modified: >>>> trunk/test_suite/system_tests/relax_disp.py >>>> >>>> Modified: trunk/test_suite/system_tests/relax_disp.py >>>> URL: >>>> http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=22198&r1=22197&r2=22198&view=diff >>>> ============================================================================== >>>> --- trunk/test_suite/system_tests/relax_disp.py (original) >>>> +++ trunk/test_suite/system_tests/relax_disp.py Tue Feb 18 12:19:41 2014 >>>> @@ -264,6 +264,21 @@ >>>> relax_disp.Relax_disp.opt_max_iterations = 1000 >>>> relax_disp.Relax_disp(pipe_name="origin - relax_disp (Thu Jan 2 >>>> 13:46:44 2014)", pipe_bundle="relax_disp (Thu Jan 2 13:46:44 2014)", >>>> results_dir=self.tmpdir, models=['R2eff', 'No Rex', 'CR72', 'NS CPMG >>>> 2-site expanded'], 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) >>>> >>>> + >>>> + def test_bug_21665_cpmg_two_fields_two_delaytimes_fail(self): >>>> + """U{Bug #21665<https://gna.org/bugs/?21665>} catch, the failure >>>> due to a a CPMG analysis recorded at two fields at two delay times.""" >>>> + >>>> + # Clear the data store. >>>> + self.interpreter.reset() >>>> + >>>> + # Load the state. >>>> + state = status.install_path + >>>> sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_21665.bz2' >>>> + self.interpreter.state.load(state, force=True) >>>> + >>>> + # Execute the auto-analysis (fast). >>>> + relax_disp.Relax_disp.opt_func_tol = 1e-5 >>>> + relax_disp.Relax_disp.opt_max_iterations = 1000 >>>> + relax_disp.Relax_disp(pipe_name="compare_128_FT_R2eff", >>>> pipe_bundle="cpmg_disp_sod1d90a", 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) >>>> >>>> >>>> def test_curve_type_cpmg_fixed_time(self): >>>> >>>> >>>> _______________________________________________ >>>> 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
