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
