Re: r22198 - /trunk/test_suite/system_tests/relax_disp.py -- February 18, 2014 - 15:50

Ah, that's the problem.  You'll need to replace this with one of the
relaxation dispersion loops, have a look at the loop_*() functions in
specific_analyses.relax_disp.disp_data.  You could for example use the
loop_exp_frq_offset_point() and then count the time points for each of
these iterations.  This is only one of many alternatives.

If you feel more adventurous, you could make the count_relax_times()
function dependent on ei, mi, oi, and di (see the module docstring for
a description of this:
http://www.nmr-relax.com/api/3.1/specific_analyses.relax_disp.disp_data-module.html).
 You would then have to delete the use of loop_time() and do something
as in the insignificance() function.

There are other ways too.  The key is to loop over each experiment
collection of {ei, mi, oi, di} and check the times for each.  If there
is only one time for the experiment block, then this is the 2-point
calculation.  If there is more, then exponential curve fitting is
needed.  If one block of {ei, mi, oi, di} is 2-point and another is
exponential, then relax will fail.  But this type of data combination
is very unlikely to ever be encountered and we can deal with that when
a user complains ;)

Anyway, have a look at specific_analyses.relax_disp.disp_data for
inspiration, as all the code you need to write can be copied from
various functions of that module.  The logic you need is repeated in
about 10 functions there.  I hope this helps.

Regards,

Edward




On 18 February 2014 15:35, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx> 
wrote:
> 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 <edward@xxxxxxxxxxxxx>:
> > 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 <tlinnet@xxxxxxxxxxxxx> 
> > 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 <tlinnet@xxxxxxxxxxxxx>:
> > > > 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  <tlinnet@xxxxxxxxxxxxx>:
> > > > > 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):
> > > > >
> > > > >
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