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 > > 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