Re: Regarding systemtest: ./relax -s Relax_disp.test_bug_21344_sparse_time_spinlock_acquired_r1rho_fail_relax_disp -- February 27, 2014 - 12:37

Actually, by grepping the source code:

$ grep "find_intensity_keys([a-z]" -r . --exclude-dir=.svn

I can see many places where find_intensity_keys() is incorrectly
called!  I think it's obvious that this function came before
R1rho-type data was supported.  Looking further, the
return_intensity() function is also deficient for the offset value!
Almost everywhere where find_intensity_keys() is called is incorrectly
implemented (excluding the specific_analyses.relax_disp.nessy module
as NESSY does not support R1rho data)!  These should all be fixed
otherwise problems will appear in your analysis later on.

Thinking about the problem even more, I can see that only one key is
ever used when calling find_intensity_keys().  The purpose of having a
list of keys has been permanently lost - I remember implementing this
as a feature earlier in the relax_disp branch development but the
reason for it no longer exists.  As a clean solution, I would suggest:

- Renaming the function to find_intensity_key() and have it return a
single value.
- Have the find_intensity_key() function raise a RelaxError if more
than one key is found.
- Modify all of the code calling find_intensity_key() to expect and
handle a single key.
- Modify the return_intensity() function to be more like the
average_intensity() function in that the offset argument is supported.

This solution would be much more maintainable in the future.  What do you 
think?

Regards,

Edward

On 27 February 2014 12:08, Edward d'Auvergne <edward.dauvergne@xxxxxxxxx> 
wrote:
> Hi,
>
> This looks like another rather stupid typo/mistake :)  I added a print
> statement for the int_keys variable and ran the test.  There should
> only be one key for a given {exp_type, frq, offset, point, time}
> metadata set, but the printout shows this not to be the case.  If you
> carefully look at the find_intensity_keys() call, you will see that
> one of these 5 bits of information are not sent in as an argument ;)
>
> Regards,
>
> Edward
>
>
>
>
> On 27 February 2014 11:38, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx> 
> wrote:
> > Hi Edward.
> >
> > When I run:
> > ./relax -s 
> > Relax_disp.test_bug_21344_sparse_time_spinlock_acquired_r1rho_fail_relax_disp
> >
> > I get:
> > -------------------
> > Parameter values: [2.4392597217423719, 149801.17120634759]
> > Function value:   252.36349493927844
> > Iterations:       135
> > Function calls:   281
> > Gradient calls:   0
> > Hessian calls:    0
> > Warning:          None
> >
> >
> > relax> eliminate(function=None, args=None)
> >
> > relax> monte_carlo.setup(number=5)
> >
> > relax> monte_carlo.create_data(method='back_calc')
> > Traceback (most recent call last):
> >   File 
> > "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/test_suite/system_tests/relax_disp.py",
> > line 284, in 
> > test_bug_21344_sparse_time_spinlock_acquired_r1rho_fail_relax_disp
> >     relax_disp.Relax_disp(pipe_name='base pipe',
> > pipe_bundle='relax_disp', 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 118, in __init__
> >     self.run()
> >   File 
> > "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/auto_analyses/relax_disp.py",
> > line 471, in run
> >     self.optimise(model=model)
> >   File 
> > "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/auto_analyses/relax_disp.py",
> > line 379, in optimise
> >     self.interpreter.monte_carlo.create_data()
> >   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/monte_carlo.py",
> > line 113, in create_data
> >     pack_sim_data(data_index, random)
> >   File 
> > "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/specific_analyses/relax_disp/api.py",
> > line 1609, in sim_pack_data
> >     raise RelaxError("Monte Carlo simulation data for the key '%s'
> > already exists." % int_key)
> > RelaxError: RelaxError: Monte Carlo simulation data for the key
> > '1_0_46_0' already exists.
> >
> > ---------------------
> >
> > I have looked into:
> > specific_analyses/relax_disp/api.py
> >
> > There it is:
> > ----------------------------------------------
> >     def sim_pack_data(self, data_id, sim_data):
> >         """Pack the Monte Carlo simulation data.
> >
> >         @param data_id:     The tuple of the spin container and the
> > exponential curve identifying key, as yielded by the base_data_loop()
> > generator method.
> >         @type data_id:      SpinContainer instance and float
> >         @param sim_data:    The Monte Carlo simulation data.
> >         @type sim_data:     list of float
> >         """
> >
> >         # The R2eff model (with peak intensity base data).
> >         if cdp.model_type == 'R2eff':
> >             # Unpack the data.
> >             spin, exp_type, frq, offset, point = data_id
> >
> >             # Initialise the data structure if needed.
> >             if not hasattr(spin, 'intensity_sim'):
> >                 spin.intensity_sim = {}
> >
> >             # Loop over each time point.
> >             ti = 0
> >             for time in loop_time(exp_type=exp_type, frq=frq,
> > offset=offset, point=point):
> >                 # Get the intensity keys.
> >                 int_keys = find_intensity_keys(exp_type=exp_type,
> > frq=frq, point=point, time=time)
> >
> >                 # Loop over the intensity keys.
> >                 for int_key in int_keys:
> >                     # Test if the simulation data point already exists.
> >                     if int_key in spin.intensity_sim:
> >                         raise RelaxError("Monte Carlo simulation data
> > for the key '%s' already exists." % int_key)
> >
> >                     # Initialise the list.
> >                     spin.intensity_sim[int_key] = []
> >
> >                     # Loop over the simulations, appending the
> > corresponding data.
> >                     for i in range(cdp.sim_number):
> >                         spin.intensity_sim[int_key].append(sim_data[i][ti])
> >
> >                 # Increment the time index.
> >                 ti += 1
> > ---------------------
> >
> > For me, this looks okay.
> >
> > Do you have an Idea why this is not working?
> >
> > Best
> > Troels