Hi, I forgot to mention that the unit test is like the system test but it is designed to only test the behaviour of a single function or method.
Regards, Edward On 19 February 2014 13:58, Edward d'Auvergne <[email protected]> wrote: > Hi, > > Looking at your save state > test_suite/shared_data/dispersion/bug_21665.bz2 and your printout, it > looks like the specific_analyses.relax_disp. > disp_data.loop_exp_frq_offset_point_time() function is not operating > correctly. Therefore the bug must be in one of the loop_() functions! > You could, if you feel adventurous, create unit tests for the loop_() > functions by simply loading the bug_21665.bz2 saved state, executing > the loop_() function, and then checking that the values and indices > are what you would expect. This is like in your message, but instead > of using a print() call, you use an assertEqual() call and have all > the values you would expect stored in a list at the start of the unit > test function. These unit tests would really speed up the debugging > by being much closer to the bug. I'll create the unit test > directories and empty files required now - you can chose to use them > if you wish. > > As for storing the data, that is not the problem. The base is the > experiment ID string which is used as a key in dictionaries for each > piece of information (experiment type, spectrometer frequency, offset, > dispersion point, and time point are all separate dictionaries). The > data storage is quite basic as you can see in the saved state. This > has the advantage of being stable over the long term for save state > compatibility between different relax versions. The data storage in > the relax data store is designed to be as simple as possible. The > problem is the construction of loops over this data - this is the > complicated part. Obviously, for the data you have, one or more of > these loops are not functioning correctly. You are getting much > closer to the real issue! If you have unit tests for each of the > loop_() functions, then once these pass you should eliminate all > issues with this data combination. > > Regards, > > Edward > > > On 19 February 2014 12:29, Troels Emtekær Linnet <[email protected]> > wrote: >> Hi Edward. >> >> If i use the function: >> >> for exp_type, frq, offset, point, time, ei, mi, oi, di, ti in >> specific_analyses.relax_disp.disp_data.loop_exp_frq_offset_point_time(return_indices=True): >> print exp_type, frq, offset, point, time, ei, mi, oi, di, ti >> >> Where i guess that: >> ei = experiment index >> mi = frequency index >> oi = offset index >> di = dispersion index >> ti = time index >> >> SQ CPMG 499862140.0 0.0 50.0 0.04 0 0 0 0 0 >> SQ CPMG 499862140.0 0.0 50.0 0.06 0 0 0 0 1 >> SQ CPMG 499862140.0 0.0 100.0 0.04 0 0 0 1 0 >> SQ CPMG 499862140.0 0.0 100.0 0.06 0 0 0 1 1 >> SQ CPMG 499862140.0 0.0 150.0 0.04 0 0 0 2 0 >> SQ CPMG 499862140.0 0.0 150.0 0.06 0 0 0 2 1 >> SQ CPMG 499862140.0 0.0 200.0 0.04 0 0 0 3 0 >> SQ CPMG 499862140.0 0.0 200.0 0.06 0 0 0 3 1 >> SQ CPMG 499862140.0 0.0 250.0 0.04 0 0 0 4 0 >> SQ CPMG 499862140.0 0.0 250.0 0.06 0 0 0 4 1 >> SQ CPMG 499862140.0 0.0 300.0 0.04 0 0 0 5 0 >> SQ CPMG 499862140.0 0.0 300.0 0.06 0 0 0 5 1 >> SQ CPMG 499862140.0 0.0 350.0 0.04 0 0 0 6 0 >> SQ CPMG 499862140.0 0.0 350.0 0.06 0 0 0 6 1 >> SQ CPMG 499862140.0 0.0 400.0 0.04 0 0 0 7 0 >> SQ CPMG 499862140.0 0.0 400.0 0.06 0 0 0 7 1 >> SQ CPMG 499862140.0 0.0 450.0 0.04 0 0 0 8 0 >> SQ CPMG 499862140.0 0.0 450.0 0.06 0 0 0 8 1 >> SQ CPMG 499862140.0 0.0 500.0 0.04 0 0 0 9 0 >> SQ CPMG 499862140.0 0.0 500.0 0.06 0 0 0 9 1 >> SQ CPMG 499862140.0 0.0 550.0 0.04 0 0 0 10 0 >> SQ CPMG 499862140.0 0.0 550.0 0.06 0 0 0 10 1 >> SQ CPMG 499862140.0 0.0 600.0 0.04 0 0 0 11 0 >> SQ CPMG 499862140.0 0.0 600.0 0.06 0 0 0 11 1 >> SQ CPMG 499862140.0 0.0 650.0 0.04 0 0 0 12 0 >> SQ CPMG 499862140.0 0.0 650.0 0.06 0 0 0 12 1 >> SQ CPMG 499862140.0 0.0 700.0 0.04 0 0 0 13 0 >> SQ CPMG 499862140.0 0.0 700.0 0.06 0 0 0 13 1 >> SQ CPMG 499862140.0 0.0 800.0 0.04 0 0 0 14 0 >> SQ CPMG 499862140.0 0.0 800.0 0.06 0 0 0 14 1 >> SQ CPMG 499862140.0 0.0 900.0 0.04 0 0 0 15 0 >> SQ CPMG 499862140.0 0.0 900.0 0.06 0 0 0 15 1 >> SQ CPMG 499862140.0 0.0 1000.0 0.04 0 0 0 16 0 >> SQ CPMG 499862140.0 0.0 1000.0 0.06 0 0 0 16 1 >> SQ CPMG 599890858.7 0.0 33.333 0.04 0 1 0 0 0 >> SQ CPMG 599890858.7 0.0 33.333 0.06 0 1 0 0 1 >> SQ CPMG 599890858.7 0.0 66.667 0.04 0 1 0 1 0 >> SQ CPMG 599890858.7 0.0 66.667 0.06 0 1 0 1 1 >> SQ CPMG 599890858.7 0.0 100.0 0.04 0 1 0 2 0 >> SQ CPMG 599890858.7 0.0 100.0 0.06 0 1 0 2 1 >> SQ CPMG 599890858.7 0.0 133.333 0.04 0 1 0 3 0 >> SQ CPMG 599890858.7 0.0 133.333 0.06 0 1 0 3 1 >> SQ CPMG 599890858.7 0.0 166.667 0.04 0 1 0 4 0 >> SQ CPMG 599890858.7 0.0 166.667 0.06 0 1 0 4 1 >> SQ CPMG 599890858.7 0.0 200.0 0.04 0 1 0 5 0 >> SQ CPMG 599890858.7 0.0 200.0 0.06 0 1 0 5 1 >> SQ CPMG 599890858.7 0.0 233.333 0.04 0 1 0 6 0 >> SQ CPMG 599890858.7 0.0 233.333 0.06 0 1 0 6 1 >> SQ CPMG 599890858.7 0.0 266.667 0.04 0 1 0 7 0 >> SQ CPMG 599890858.7 0.0 266.667 0.06 0 1 0 7 1 >> SQ CPMG 599890858.7 0.0 300.0 0.04 0 1 0 8 0 >> SQ CPMG 599890858.7 0.0 300.0 0.06 0 1 0 8 1 >> SQ CPMG 599890858.7 0.0 333.333 0.04 0 1 0 9 0 >> SQ CPMG 599890858.7 0.0 333.333 0.06 0 1 0 9 1 >> SQ CPMG 599890858.7 0.0 366.667 0.04 0 1 0 10 0 >> SQ CPMG 599890858.7 0.0 366.667 0.06 0 1 0 10 1 >> SQ CPMG 599890858.7 0.0 400.0 0.04 0 1 0 11 0 >> SQ CPMG 599890858.7 0.0 400.0 0.06 0 1 0 11 1 >> SQ CPMG 599890858.7 0.0 466.667 0.04 0 1 0 12 0 >> SQ CPMG 599890858.7 0.0 466.667 0.06 0 1 0 12 1 >> SQ CPMG 599890858.7 0.0 533.333 0.04 0 1 0 13 0 >> SQ CPMG 599890858.7 0.0 533.333 0.06 0 1 0 13 1 >> SQ CPMG 599890858.7 0.0 666.667 0.04 0 1 0 14 0 >> SQ CPMG 599890858.7 0.0 666.667 0.06 0 1 0 14 1 >> SQ CPMG 599890858.7 0.0 866.667 0.04 0 1 0 15 0 >> SQ CPMG 599890858.7 0.0 866.667 0.06 0 1 0 15 1 >> SQ CPMG 599890858.7 0.0 1000.0 0.04 0 1 0 16 0 >> SQ CPMG 599890858.7 0.0 1000.0 0.06 0 1 0 16 1 >> >> Then we see that the dispersion point of 50.0 exist for time 0.04 and 0.06. >> That is not true, this point only exists for time point 0.04 >> >> Maybe I am reading your suggestion a little wrong. >> >> I am a little un-sure if relax stores the data in the wrong way, and >> this should be handled. >> Or if the problem is the "checks" before the calculation. >> >> And then I guess that there are some looping functions which collect >> the data, before >> doing a calculation. >> >> >> >> >> >> >> 2014-02-18 15:50 GMT+01:00 Edward d'Auvergne <[email protected]>: >>> 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 <[email protected]> >>> 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 <[email protected]>: >>>>> 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 <[email protected]> >>>>> 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 <[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 _______________________________________________ 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
