Re: r22222 - /trunk/specific_analyses/relax_disp/disp_data.py -- February 21, 2014 - 10:37

Hi,

I saw this, and thought that the solution you found for fixing the
unit test was too simple.  I think that if you carefully look at what
the loop_*() function in your unit test returns, you will see that
there will still be strange metadata combinations.  To simplify
testing, the core of the unit test can be put into a relax script:

"""
from specific_analyses.relax_disp.disp_data import
loop_exp_frq_offset_point_time

# Load the state.
statefile = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_21665.bz2'
state.load_state(statefile, force=True)
for exp_type, frq, offset, point, time, ei, mi, oi, di, ti in
loop_exp_frq_offset_point_time(return_indices=True):
    print(exp_type, frq, offset, point, time, ei, mi, oi, di, ti)
"""

You could also try each of the loop_() functions one by one and see
what they yield.  It should be logical what the results should be for
the data in your save file.  It should be exactly what is shown in the
GUI (open the 'bug_21665.bz2' file in the GUI and associate it with a
new analysis).  For testing, you could create a list of lists of the
values in the 'Spectra list' GUI element and use that in the unit
tests, checking all elements of the loop for correctness.  You should
also check that the number of iterations of the loop is correct (by
maybe running the loop once first to count all, and then running a
second time to check the values).

To pin-point the problem, I would recommend creating a few more unit
tests.  These can be easily created by copy-and-paste.  The first
target would be the loop_exp() function (so the test could be called
test_loop_exp()).  From your data in the GUI, this should return a
single value of 'SQ CPMG'.

Then you could copy this and try the loop_exp_frq() function (the test
name could be test_loop_exp_frq()).  This should have two iterations
and have the values of:

[['SQ CPMG', 499862140.0],
 ['SQ CPMG', 599890858.69999993]]

Then the loop_exp_frq_offset() function (with the test name
test_loop_exp_frq_offset()) could be created by copying and pasting
and checking for exactly the same values - as you have no offsets set.
 So the number of iterations is 2, and the values are as in the list
of lists above.

The same logic can be applied to each loop_*() function and a series
of unit tests created in quick succession.  Such a network of simple
but comprehensive unit tests will reveal exactly where the bug is!
Checking all of the loop_*() functions will really pin-point the
problem, as these functions all call each other for their looping.

To help you get started, I'll add a first test :)  ...  Done (see
http://article.gmane.org/gmane.science.nmr.relax.scm/20001).  Feel
free top copy and paste this test for the other loop_*() functions.

Regards,

Edward




On 20 February 2014 19:06, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx> 
wrote:
> Hi Edward.
>
> I now seem to have problems how to solve:
> relax -s 
> Relax_disp.test_bug_21665_cpmg_two_fields_two_delaytimes_fail_relax_disp
>
> -------
> Traceback (most recent call last):
>   File 
> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/test_suite/system_tests/relax_disp.py",
> line 295, in test_bug_21665_cpmg_two_fields_two_delaytimes_fail_relax_disp
>     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
> --------------
>
> I can point the error stems from:
>
> 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))
>
> ---------------
>             # Loop over each spectrometer frequency and dispersion point.
>             for exp_type, frq, offset, point in loop_exp_frq_offset_point():
> ....
>                 for time in cdp.relax_time_list:
>                     values.append(average_intensity(spin=spin,
> exp_type=exp_type, frq=frq, offset=offset, point=point, time=time,
> sim_index=sim_index))
>                     errors.append(average_intensity(spin=spin,
> exp_type=exp_type, frq=frq, offset=offset, point=point, time=time,
> error=True))
>                     times.append(time)
> -------------
>
> I think this should be solvable with something like:
>
>
> ---------------
>             # Loop over each spectrometer frequency and dispersion point.
>             for exp_type, frq, offset, point in
> loop_exp_frq_offset_point_time():
> ....
>             values.append(average_intensity(spin=spin,
> exp_type=exp_type, frq=frq, offset=offset, point=point, time=time,
> sim_index=sim_index))
>             errors.append(average_intensity(spin=spin,
> exp_type=exp_type, frq=frq, offset=offset, point=point, time=time,
> error=True))
>             times.append(time)
> -------------
>
> What do you think ?
>
>
> 2014-02-20 18:44 GMT+01:00 Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx>:
> > Hi Edward.
> >
> > I found that the main error was the return of the dispersion points
> > from the function loop_point().
> >
> > It seemed that the minimal change would be to add an extra check in
> > this function, and this
> > extra check should be dependent on the time point.
> >
> > And hence i modified the loop_point() to take time as an argument, and
> > switching the order
> > would give me the time point.
> >
> > Best
> > Troels
> >
> >
> > 2014-02-20 18:27 GMT+01:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> > > Hi Troels,
> > >
> > > Is there a reason for switching the order?  It's useful to have that
> > > in the commit message too.  I can see they are switched from the code
> > > that was changed, but I cannot see why.
> > >
> > > Cheers,
> > >
> > > Edward
> > >
> > >
> > >
> > > On 20 February 2014 18:16,  <tlinnet@xxxxxxxxxxxxx> wrote:
> > > > Author: tlinnet
> > > > Date: Thu Feb 20 18:16:51 2014
> > > > New Revision: 22222
> > > >
> > > > URL: http://svn.gna.org/viewcvs/relax?rev=22222&view=rev
> > > > Log:
> > > > Switched the looping over time points and dispersion points.
> > > >
> > > > Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG 
> > > > analysis with two fields at two delay times.
> > > >
> > > > Modified:
> > > >     trunk/specific_analyses/relax_disp/disp_data.py
> > > >
> > > > Modified: trunk/specific_analyses/relax_disp/disp_data.py
> > > > URL: 
> > > > http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/disp_data.py?rev=22222&r1=22221&r2=22222&view=diff
> > > > ==============================================================================
> > > > --- trunk/specific_analyses/relax_disp/disp_data.py (original)
> > > > +++ trunk/specific_analyses/relax_disp/disp_data.py Thu Feb 20 18:16:51 
> > > > 2014
> > > > @@ -869,10 +869,10 @@
> > > >          for frq, mi in loop_frq(return_indices=True):
> > > >              # Then loop over the offset data.
> > > >              for offset, oi in loop_offset(exp_type=exp_type, frq=frq, 
> > > > return_indices=True):
> > > > -                # Then the dispersion points.
> > > > -                for point, di in loop_point(exp_type=exp_type, frq=frq, 
> > > > offset=offset, return_indices=True):
> > > > -                    # Finally the relaxation times.
> > > > -                    for time, ti in loop_time(return_indices=True):
> > > > +                # Then the relaxation times.
> > > > +                for time, ti in loop_time(return_indices=True):
> > > > +                    # Finally the dispersion points.
> > > > +                    for point, di in loop_point(exp_type=exp_type, 
> > > > frq=frq, offset=offset, time=time, return_indices=True):
> > > >                          # Yield the data.
> > > >                          if return_indices:
> > > >                              yield exp_type, frq, offset, point, time, 
> > > > ei, mi, oi, di, ti
> > > >
> > > >
> > > > _______________________________________________
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