Re: Regarding systemtest: ./relax -s Relax_disp.test_bug_21344_sparse_time_spinlock_acquired_r1rho_fail_relax_dispRe: Regarding systemtest: ./relax -s Relax_disp.test_bug_21344_sparse_time_spinlock_acquired_r1rho_fail_relax_dispActually, 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