Re: r21920 - /trunk/test_suite/system_tests/relax_disp.pyRe: r21920 - /trunk/test_suite/system_tests/relax_disp.pyWe should then definitely have this tested in the test suite! I just
had a look at it and will commit the fix very soon. The problem is
that I have recently introduced the spin-lock (or hard pulse for the
CPMG) offset dimension into all of the dispersion data structures used
in the target functions. But the grid_search_setup() method was not
updated correctly for this. Note the loop_exp_frq_point() function
call, the fix is to replace it with loop_exp_frq_offset_point() to
loop over all of these!
Cheers,
Edward
On 10 December 2013 11:43, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx> wrote:
> Hi Edward.
>
> I can say that running this:
> relax ./test_suite/shared_data/dispersion/r1rho_on_res_m61/r2eff_calc.py
>
> Give the same error.
> File "/Users/tlinnet/software/relax_trunk/pipe_control/minimise.py", line
> 152, in grid_search
> grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints,
> verbosity=verbosity)
> File
> "/Users/tlinnet/software/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
> "/Users/tlinnet/software/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
> "/Users/tlinnet/software/relax_trunk/specific_analyses/relax_disp/api.py",
> line 357, in _minimise_r2eff
> grid_size, inc_new, lower_new, upper_new =
> grid_search_setup(spins=[spin], spin_ids=[spin_id],
> param_vector=param_vector, lower=lower, upper=upper, inc=inc,
> scaling_matrix=scaling_matrix)
> File
> "/Users/tlinnet/software/relax_trunk/specific_analyses/relax_disp/optimisation.py",
> line 282, in grid_search_setup
> lower_new.append(lower[i] / scaling_matrix[i, i])
> IndexError: list index out of range
>
>
>
>
> 2013/12/10 Edward d'Auvergne <edward@xxxxxxxxxxxxx>
>>
>> Hi,
>>
>> I saw that, but I'm not sure why it is saying that. Maybe you should
>> add some debugging printouts in the grid_search_setup() function and
>> see what is happening? It won't be because of the missing R1 data. I
>> would suggest that if you would like to develop the code for
>> optimising R1 as a parameter of the R1rho models (i.e. all of them),
>> that we should create a special branch for that. I know exactly what
>> needs to be done and I can direct you in the right direction. But it
>> needs to be developed in a branch as it will be quite disruptive.
>>
>> Regards,
>>
>> Edward
>>
>>
>>
>> On 10 December 2013 09:56, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx>
>> wrote:
>> > Hi Edward.
>> >
>> > I now receive this error:
>> > relax -s Relax_disp.test_r1rho_kjaergaard
>> >
>> > But I guess this is expected, since I do not load any R1 data in. ?
>> >
>> > Best
>> > Troels
>> > ---------
>> > relax> relax_disp.select_model(model='R2eff')
>> > R2eff/R1rho value and error determination.
>> >
>> >
>> > Optimisation
>> > ============
>> >
>> >
>> > Nesting and model equivalence checks
>> > ------------------------------------
>> >
>> > No model nesting or model equivalence detected.
>> >
>> > relax> grid_search(lower=None, upper=None, inc=4, constraints=True,
>> > verbosity=1)
>> > Traceback (most recent call last):
>> > File
>> >
>> > "/Users/tlinnet/software/relax_trunk/test_suite/system_tests/relax_disp.py",
>> > line 2591, in test_r1rho_kjaergaard
>> > relax_disp.Relax_disp(pipe_name=pipe_name, pipe_bundle=pipe_bundle,
>> > results_dir=ds.tmpdir, models=MODELS, grid_inc=GRID_INC,
>> > mc_sim_num=MC_NUM,
>> > modsel=MODSEL)
>> > File
>> > "/Users/tlinnet/software/relax_trunk/auto_analyses/relax_disp.py",
>> > line 116, in __init__
>> > self.run()
>> > File
>> > "/Users/tlinnet/software/relax_trunk/auto_analyses/relax_disp.py",
>> > line 451, in run
>> > self.optimise(model=model)
>> > File
>> > "/Users/tlinnet/software/relax_trunk/auto_analyses/relax_disp.py",
>> > line 350, in optimise
>> > self.interpreter.grid_search(inc=self.grid_inc)
>> > File "/Users/tlinnet/software/relax_trunk/prompt/uf_objects.py", line
>> > 221,
>> > in __call__
>> > self._backend(*new_args, **uf_kargs)
>> > File "/Users/tlinnet/software/relax_trunk/pipe_control/minimise.py",
>> > line
>> > 152, in grid_search
>> > grid_search(lower=lower, upper=upper, inc=inc,
>> > constraints=constraints,
>> > verbosity=verbosity)
>> > File
>> >
>> > "/Users/tlinnet/software/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
>> >
>> > "/Users/tlinnet/software/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
>> >
>> > "/Users/tlinnet/software/relax_trunk/specific_analyses/relax_disp/api.py",
>> > line 357, in _minimise_r2eff
>> > grid_size, inc_new, lower_new, upper_new =
>> > grid_search_setup(spins=[spin], spin_ids=[spin_id],
>> > param_vector=param_vector, lower=lower, upper=upper, inc=inc,
>> > scaling_matrix=scaling_matrix)
>> > File
>> >
>> > "/Users/tlinnet/software/relax_trunk/specific_analyses/relax_disp/optimisation.py",
>> > line 282, in grid_search_setup
>> > lower_new.append(lower[i] / scaling_matrix[i, i])
>> > IndexError: list index out of range
>> >
>> >
>> > 2013/12/10 Edward d'Auvergne <edward@xxxxxxxxxxxxx>
>> >>
>> >> Ah, ok, that would explain the strangeness. Then the simple solution
>> >> would be to check that the correct data pipe type is being used at the
>> >> start of both these user functions! Then a user should never reach
>> >> this failure point.
>> >>
>> >> Regards,
>> >>
>> >> Edward
>> >>
>> >>
>> >> On 10 December 2013 09:34, Troels Emtekær Linnet
>> >> <tlinnet@xxxxxxxxxxxxx>
>> >> wrote:
>> >> > Uf...
>> >> >
>> >> > There was the error:
>> >> >
>> >> > # Set the relaxation times (in s).
>> >> > self.interpreter.relax_fit.relax_time(time=time_sl,
>> >> > spectrum_id=sp_id)
>> >> > was used instead of:
>> >> > # Set the relaxation times (in s).
>> >> >
>> >> > self.interpreter.relax_disp.relax_time(spectrum_id=sp_id,
>> >> > time=time_sl)
>> >> >
>> >> >
>> >> > 2013/12/10 Edward d'Auvergne <edward@xxxxxxxxxxxxx>
>> >> >>
>> >> >> Hi,
>> >> >>
>> >> >> That's exactly the point of failure. Maybe it would be useful to
>> >> >> create one or two simple unit tests for the get_curve_type()
>> >> >> function,
>> >> >> using some of the data in the current data pipe where your script is
>> >> >> failing. The problem is that for the experiment ID being sent into
>> >> >> it, it can only find one matching relaxation time. Are you sure
>> >> >> that
>> >> >> all data is loaded correctly?
>> >> >>
>> >> >> Regards,
>> >> >>
>> >> >> Edward
>> >> >>
>> >> >>
>> >> >>
>> >> >> On 10 December 2013 09:19, Troels Emtekær Linnet
>> >> >> <tlinnet@xxxxxxxxxxxxx>
>> >> >> wrote:
>> >> >> > Hi Edward.
>> >> >> >
>> >> >> > The function: has_exponential_exp_type() is returning
>> >> >> > False, as the get_curve_type(id) is returning: fixed time
>> >> >> >
>> >> >> > So that test look good enough for me?
>> >> >> >
>> >> >> > Is it the: fixed time which is a problem?
>> >> >> >
>> >> >> > Best
>> >> >> > Troels
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > 2013/12/10 Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx>
>> >> >> >>
>> >> >> >> Hi Edward.
>> >> >> >>
>> >> >> >> I will try to look into it today.
>> >> >> >>
>> >> >> >> Best
>> >> >> >> Troels
>> >> >> >>
>> >> >> >>
>> >> >> >> 2013/12/9 Edward d'Auvergne <edward@xxxxxxxxxxxxx>
>> >> >> >>>
>> >> >> >>> Hi Troels,
>> >> >> >>>
>> >> >> >>> Note that I will soon release relax 3.1.1 with all of the recent
>> >> >> >>> fixes
>> >> >> >>> (possibly tomorrow). This includes the 'NS MMQ 3-site', 'NS MMQ
>> >> >> >>> 3-site linear', 'NS R1rho 3-site', and 'NS R1rho 3-site linear'
>> >> >> >>> dispersion models which are now implemented, tested, and find
>> >> >> >>> similar
>> >> >> >>> results to Dmitry Korzhnev's cpmg_fit software. If the test is
>> >> >> >>> not
>> >> >> >>> functional by then, I will disable it for the release. It would
>> >> >> >>> be
>> >> >> >>> very useful to have fixed though as it looks like variable
>> >> >> >>> relaxation
>> >> >> >>> time data (SQ CPMG, MMQ CPMG, or R1rho) will all currently fail
>> >> >> >>> in
>> >> >> >>> the
>> >> >> >>> auto-analysis. I've had a look and have another hint for you -
>> >> >> >>> the
>> >> >> >>> problem is that has_exponential_exp_type() function is not
>> >> >> >>> returning
>> >> >> >>> the correct answer ;)
>> >> >> >>>
>> >> >> >>> Regards,
>> >> >> >>>
>> >> >> >>> Edward
>> >> >> >>>
>> >> >> >>>
>> >> >> >>>
>> >> >> >>> On 9 December 2013 18:12, Edward d'Auvergne
>> >> >> >>> <edward@xxxxxxxxxxxxx>
>> >> >> >>> wrote:
>> >> >> >>> > Hi,
>> >> >> >>> >
>> >> >> >>> > This is a strange failure! The auto-analysis should not be
>> >> >> >>> > running
>> >> >> >>> > the calc user function for this. That is the problem, you
>> >> >> >>> > cannot
>> >> >> >>> > run
>> >> >> >>> > the calc user function for non-constant relaxation time
>> >> >> >>> > experiments.
>> >> >> >>> > The error message is the standard one to tell the user that.
>> >> >> >>> > The
>> >> >> >>> > grid_search and minimise user functions should be used instead
>> >> >> >>> > (maybe
>> >> >> >>> > the error message can be modified to clarify this and include
>> >> >> >>> > this
>> >> >> >>> > info). But it is the auto-analysis that is running this. So
>> >> >> >>> > the
>> >> >> >>> > problem is there. relax can of course handle variable
>> >> >> >>> > relaxation
>> >> >> >>> > times for any dispersion data type.
>> >> >> >>> >
>> >> >> >>> > Regards,
>> >> >> >>> >
>> >> >> >>> > Edward
>> >> >> >>> >
>> >> >> >>> >
>> >> >> >>> >
>> >> >> >>> >
>> >> >> >>> > On 9 December 2013 18:02, Troels Emtekær Linnet
>> >> >> >>> > <tlinnet@xxxxxxxxxxxxx>
>> >> >> >>> > wrote:
>> >> >> >>> >> Hi Edward.
>> >> >> >>> >>
>> >> >> >>> >> The R1rho data is not constant time.
>> >> >> >>> >>
>> >> >> >>> >> I have only included the models:
>> >> >> >>> >> MODELS = ['R2eff', 'No Rex', 'DPL94']
>> >> >> >>> >>
>> >> >> >>> >> I have set it up, to find a solution for analysing R1rho
>> >> >> >>> >> data,
>> >> >> >>> >> where
>> >> >> >>> >> R1 data
>> >> >> >>> >> has not been acquired, but for
>> >> >> >>> >> different
>> >> >> >>> >>
>> >> >> >>> >> It actually also fails at the moment, and will probably do
>> >> >> >>> >> for
>> >> >> >>> >> some
>> >> >> >>> >> time.
>> >> >> >>> >>
>> >> >> >>> >> --------
>> >> >> >>> >> relax -s Relax_disp.test_r1rho_kjaergaar
>> >> >> >>> >>
>> >> >> >>> >> relax> calc(verbosity=1)
>> >> >> >>> >> Traceback (most recent call last):
>> >> >> >>> >> File
>> >> >> >>> >>
>> >> >> >>> >>
>> >> >> >>> >>
>> >> >> >>> >>
>> >> >> >>> >> "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/test_suite/system_tests/relax_disp.py",
>> >> >> >>> >> line 2581, in test_r1rho_kjaergaard
>> >> >> >>> >> relax_disp.Relax_disp(pipe_name=pipe_name,
>> >> >> >>> >> pipe_bundle=pipe_bundle,
>> >> >> >>> >> results_dir=ds.tmpdir, models=MODELS, grid_inc=GRID_INC,
>> >> >> >>> >> mc_sim_num=MC_NUM,
>> >> >> >>> >> modsel=MODSEL)
>> >> >> >>> >> 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 447, in run
>> >> >> >>> >> self.interpreter.calc()
>> >> >> >>> >> 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 'R1rho' is not of the
>> >> >> >>> >> fixed
>> >> >> >>> >> relaxation time period data type.
>> >> >> >>> >>
>> >> >> >>> >> --------------
>> >> >> >>> >>
>> >> >> >>> >> Is the R1rho analysis only implemented for fixed time
>> >> >> >>> >> periods?
>> >> >> >>> >>
>> >> >> >>> >> Best
>> >> >> >>> >> Troels
>> >> >> >>> >>
>> >> >> >>> >>
>> >> >> >>> >>
>> >> >> >>> >> 2013/12/9 Edward d'Auvergne <edward@xxxxxxxxxxxxx>
>> >> >> >>> >>>
>> >> >> >>> >>> Hi Troels,
>> >> >> >>> >>>
>> >> >> >>> >>> When looking at this data and analysis, remember that I have
>> >> >> >>> >>> not
>> >> >> >>> >>> implemented Dmitry Korzhnev's "correction" for constant time
>> >> >> >>> >>> R1rho
>> >> >> >>> >>> data. I don't know if that was used in the original
>> >> >> >>> >>> publication
>> >> >> >>> >>> for
>> >> >> >>> >>> your data. More details are given in the 'To do' section of
>> >> >> >>> >>> the
>> >> >> >>> >>> manual (I only recently added this info). I also don't know
>> >> >> >>> >>> what
>> >> >> >>> >>> the
>> >> >> >>> >>> rest of the field think of his correction and how it applies
>> >> >> >>> >>> to
>> >> >> >>> >>> later
>> >> >> >>> >>> models from the Palmer group.
>> >> >> >>> >>>
>> >> >> >>> >>> Regards,
>> >> >> >>> >>>
>> >> >> >>> >>> Edward
>> >> >> >>> >>>
>> >> >> >>> >>>
>> >> >> >>> >>>
>> >> >> >>> >>> On 9 December 2013 17:49, <tlinnet@xxxxxxxxxxxxx> wrote:
>> >> >> >>> >>> > Author: tlinnet
>> >> >> >>> >>> > Date: Mon Dec 9 17:49:49 2013
>> >> >> >>> >>> > New Revision: 21920
>> >> >> >>> >>> >
>> >> >> >>> >>> > URL: http://svn.gna.org/viewcvs/relax?rev=21920&view=rev
>> >> >> >>> >>> > Log:
>> >> >> >>> >>> > Added system test for the analysis of optimisation of the
>> >> >> >>> >>> > Kjaergaard et
>> >> >> >>> >>> > al., 2013 Off-resonance R1rho relaxation dispersion
>> >> >> >>> >>> > experiments
>> >> >> >>> >>> > using the
>> >> >> >>> >>> > 'DPL' model.
>> >> >> >>> >>> >
>> >> >> >>> >>> > Work in progress for Support Request #3083,
>> >> >> >>> >>> > (https://gna.org/support/index.php?3083) - Addition of
>> >> >> >>> >>> > Data-set
>> >> >> >>> >>> > for R1rho
>> >> >> >>> >>> > analysis.
>> >> >> >>> >>> >
>> >> >> >>> >>> > 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=21920&r1=21919&r2=21920&view=diff
>> >> >> >>> >>> >
>> >> >> >>> >>> >
>> >> >> >>> >>> >
>> >> >> >>> >>> >
>> >> >> >>> >>> >
>> >> >> >>> >>> > ==============================================================================
>> >> >> >>> >>> > --- trunk/test_suite/system_tests/relax_disp.py (original)
>> >> >> >>> >>> > +++ trunk/test_suite/system_tests/relax_disp.py Mon Dec 9
>> >> >> >>> >>> > 17:49:49
>> >> >> >>> >>> > 2013
>> >> >> >>> >>> > @@ -2450,6 +2450,137 @@
>> >> >> >>> >>> >
>> >> >> >>> >>> > self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].chi2,
>> >> >> >>> >>> > 0.030959849811015544, 3)
>> >> >> >>> >>> >
>> >> >> >>> >>> >
>> >> >> >>> >>> > + def test_r1rho_kjaergaard(self):
>> >> >> >>> >>> > + """Optimisation of the Kjaergaard et al., 2013
>> >> >> >>> >>> > Off-resonance
>> >> >> >>> >>> > R1rho relaxation dispersion experiments using the 'DPL'
>> >> >> >>> >>> > model.
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + This uses the data from Kjaergaard's paper at
>> >> >> >>> >>> > U{DOI:
>> >> >> >>> >>> > 10.1021/bi4001062<http://dx.doi.org/10.1021/bi4001062>}.
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + """
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # The path to the data files.
>> >> >> >>> >>> > + data_path = status.install_path +
>> >> >> >>> >>> >
>> >> >> >>> >>> >
>> >> >> >>> >>> >
>> >> >> >>> >>> >
>> >> >> >>> >>> > sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013'
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # Set pipe name, bundle and type.
>> >> >> >>> >>> > + pipe_name = 'base pipe'
>> >> >> >>> >>> > + pipe_bundle = 'relax_disp'
>> >> >> >>> >>> > + pipe_type= 'relax_disp'
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # Create the data pipe.
>> >> >> >>> >>> > + self.interpreter.pipe.create(pipe_name=pipe_name,
>> >> >> >>> >>> > bundle=pipe_bundle, pipe_type=pipe_type)
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # Read the spins.
>> >> >> >>> >>> > +
>> >> >> >>> >>> >
>> >> >> >>> >>> >
>> >> >> >>> >>> >
>> >> >> >>> >>> >
>> >> >> >>> >>> > self.interpreter.spectrum.read_spins(file='1_0_46_0_max_standard.ser',
>> >> >> >>> >>> > dir=data_path+sep+'peak_lists')
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # Test some of the sequence.
>> >> >> >>> >>> > + self.assertEqual(len(cdp.mol), 1)
>> >> >> >>> >>> > + self.assertEqual(cdp.mol[0].name, None)
>> >> >> >>> >>> > + self.assertEqual(len(cdp.mol[0].res), 48)
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # Name the isotope for field strength scaling.
>> >> >> >>> >>> > + self.interpreter.spin.isotope(isotope='15N')
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # Set number of experiments to be used.
>> >> >> >>> >>> > + NR_exp = -1
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # Load the experiments settings file.
>> >> >> >>> >>> > + expfile =
>> >> >> >>> >>> > open(data_path+sep+'exp_parameters_sort.txt','r')
>> >> >> >>> >>> > + expfileslines = expfile.readlines()[:NR_exp]
>> >> >> >>> >>> > + expfile.close()
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # In MHz
>> >> >> >>> >>> > + yOBS = 81.050
>> >> >> >>> >>> > + # In ppm
>> >> >> >>> >>> > + yCAR = 118.078
>> >> >> >>> >>> > + centerPPM_N15 = yCAR
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + ## Read the chemical shift data.
>> >> >> >>> >>> > +
>> >> >> >>> >>> >
>> >> >> >>> >>> >
>> >> >> >>> >>> >
>> >> >> >>> >>> >
>> >> >> >>> >>> > self.interpreter.chemical_shift.read(file='1_0_46_0_max_standard.ser',
>> >> >> >>> >>> > dir=data_path+sep+'peak_lists')
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # Test the chemical shift data.
>> >> >> >>> >>> > + cs = [122.223, 122.162, 114.250, 125.852,
>> >> >> >>> >>> > 118.626,
>> >> >> >>> >>> > 117.449,
>> >> >> >>> >>> > 119.999, 122.610, 118.602, 118.291, 115.393,
>> >> >> >>> >>> > + 121.288, 117.448, 116.378, 116.316, 117.263,
>> >> >> >>> >>> > 122.211,
>> >> >> >>> >>> > 118.748,
>> >> >> >>> >>> > 118.103, 119.421, 119.317, 119.386, 117.279,
>> >> >> >>> >>> > + 122.103, 120.038, 116.698, 111.811, 118.639,
>> >> >> >>> >>> > 118.285,
>> >> >> >>> >>> > 121.318,
>> >> >> >>> >>> > 117.770, 119.948, 119.759, 118.314, 118.160,
>> >> >> >>> >>> > + 121.442, 118.714, 113.080, 125.706, 119.183,
>> >> >> >>> >>> > 120.966,
>> >> >> >>> >>> > 122.361,
>> >> >> >>> >>> > 126.675, 117.069, 120.875, 109.372, 119.811, 126.048]
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + i = 0
>> >> >> >>> >>> > + for spin, spin_id in spin_loop(return_id=True):
>> >> >> >>> >>> > + print spin.name, spin.num, spin_id,
>> >> >> >>> >>> > spin.chemical_shift,
>> >> >> >>> >>> > cs[i]
>> >> >> >>> >>> > + # Check the chemical shift.
>> >> >> >>> >>> > + self.assertEqual(spin.chemical_shift, cs[i])
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # Increment the index.
>> >> >> >>> >>> > + i += 1
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # The lock power to field, has been found in an
>> >> >> >>> >>> > calibration
>> >> >> >>> >>> > experiment.
>> >> >> >>> >>> > + spin_lock_field_strengths_Hz = {'35': 431.0,
>> >> >> >>> >>> > '39':
>> >> >> >>> >>> > 651.2,
>> >> >> >>> >>> > '41':
>> >> >> >>> >>> > 800.5, '43': 984.0, '46': 1341.11, '48': 1648.5}
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # Apply spectra settings.
>> >> >> >>> >>> > + for i in range(len(expfileslines)):
>> >> >> >>> >>> > + line=expfileslines[i]
>> >> >> >>> >>> > + if line[0] == "#":
>> >> >> >>> >>> > + continue
>> >> >> >>> >>> > + else:
>> >> >> >>> >>> > + # DIRN I deltadof2 dpwr2slock ncyc trim
>> >> >> >>> >>> > ss
>> >> >> >>> >>> > sfrq
>> >> >> >>> >>> > + DIRN = line.split()[0]
>> >> >> >>> >>> > + I = int(line.split()[1])
>> >> >> >>> >>> > + deltadof2 = line.split()[2]
>> >> >> >>> >>> > + dpwr2slock = line.split()[3]
>> >> >> >>> >>> > + ncyc = int(line.split()[4])
>> >> >> >>> >>> > + trim = float(line.split()[5])
>> >> >> >>> >>> > + ss = int(line.split()[6])
>> >> >> >>> >>> > + set_sfrq = float(line.split()[7])
>> >> >> >>> >>> > + apod_rmsd = float(line.split()[8])
>> >> >> >>> >>> > + spin_lock_field_strength =
>> >> >> >>> >>> > spin_lock_field_strengths_Hz[dpwr2slock]
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # Calculate spin_lock time
>> >> >> >>> >>> > + time_sl = 2*ncyc*trim
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # Define file name for peak list.
>> >> >> >>> >>> > + FNAME =
>> >> >> >>> >>> > "%s_%s_%s_%s_max_standard.ser"%(I,
>> >> >> >>> >>> > deltadof2,
>> >> >> >>> >>> > dpwr2slock, ncyc)
>> >> >> >>> >>> > + sp_id = "%s_%s_%s_%s"%(I, deltadof2,
>> >> >> >>> >>> > dpwr2slock,
>> >> >> >>> >>> > ncyc)
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # Load the peak intensities.
>> >> >> >>> >>> > +
>> >> >> >>> >>> > self.interpreter.spectrum.read_intensities(file=FNAME,
>> >> >> >>> >>> > dir=data_path+sep+'peak_lists', spectrum_id=sp_id,
>> >> >> >>> >>> > int_method='height')
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # Set the peak intensity errors, as
>> >> >> >>> >>> > defined
>> >> >> >>> >>> > as
>> >> >> >>> >>> > the
>> >> >> >>> >>> > baseplane RMSD.
>> >> >> >>> >>> > +
>> >> >> >>> >>> > self.interpreter.spectrum.baseplane_rmsd(error=apod_rmsd,
>> >> >> >>> >>> > spectrum_id=sp_id)
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # Set the relaxation dispersion
>> >> >> >>> >>> > experiment
>> >> >> >>> >>> > type.
>> >> >> >>> >>> > +
>> >> >> >>> >>> > self.interpreter.relax_disp.exp_type(spectrum_id=sp_id,
>> >> >> >>> >>> > exp_type='R1rho')
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # Set The spin-lock field strength, nu1,
>> >> >> >>> >>> > in
>> >> >> >>> >>> > Hz
>> >> >> >>> >>> > +
>> >> >> >>> >>> >
>> >> >> >>> >>> >
>> >> >> >>> >>> > self.interpreter.relax_disp.spin_lock_field(spectrum_id=sp_id,
>> >> >> >>> >>> > field=spin_lock_field_strength)
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # Calculating the spin-lock offset in
>> >> >> >>> >>> > ppm,
>> >> >> >>> >>> > from
>> >> >> >>> >>> > offsets
>> >> >> >>> >>> > values provided in Hz.
>> >> >> >>> >>> > + frq_N15_Hz = yOBS * 1E6
>> >> >> >>> >>> > + offset_ppm_N15 = float(deltadof2) /
>> >> >> >>> >>> > frq_N15_Hz
>> >> >> >>> >>> > *
>> >> >> >>> >>> > 1E6
>> >> >> >>> >>> > + omega_rf_ppm = centerPPM_N15 +
>> >> >> >>> >>> > offset_ppm_N15
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # Set The spin-lock offset, omega_rf, in
>> >> >> >>> >>> > ppm.
>> >> >> >>> >>> > +
>> >> >> >>> >>> >
>> >> >> >>> >>> >
>> >> >> >>> >>> > self.interpreter.relax_disp.spin_lock_offset(spectrum_id=sp_id,
>> >> >> >>> >>> > offset=omega_rf_ppm)
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # Set the relaxation times (in s).
>> >> >> >>> >>> > +
>> >> >> >>> >>> > self.interpreter.relax_fit.relax_time(time=time_sl,
>> >> >> >>> >>> > spectrum_id=sp_id)
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # Set the spectrometer frequency.
>> >> >> >>> >>> > +
>> >> >> >>> >>> > self.interpreter.spectrometer.frequency(id=sp_id,
>> >> >> >>> >>> > frq=set_sfrq, units='MHz')
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # The dispersion models.
>> >> >> >>> >>> > + MODELS = ['R2eff', 'No Rex', 'DPL94']
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # The grid search size (the number of increments
>> >> >> >>> >>> > per
>> >> >> >>> >>> > dimension).
>> >> >> >>> >>> > + GRID_INC = 4
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # The number of Monte Carlo simulations to be
>> >> >> >>> >>> > used
>> >> >> >>> >>> > for
>> >> >> >>> >>> > error
>> >> >> >>> >>> > analysis at the end of the analysis.
>> >> >> >>> >>> > + MC_NUM = 3
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # Model selection technique.
>> >> >> >>> >>> > + MODSEL = 'AIC'
>> >> >> >>> >>> > +
>> >> >> >>> >>> > + # Run the analysis.
>> >> >> >>> >>> > + relax_disp.Relax_disp(pipe_name=pipe_name,
>> >> >> >>> >>> > pipe_bundle=pipe_bundle, results_dir=ds.tmpdir,
>> >> >> >>> >>> > models=MODELS,
>> >> >> >>> >>> > grid_inc=GRID_INC, mc_sim_num=MC_NUM, modsel=MODSEL)
>> >> >> >>> >>> > +
>> >> >> >>> >>> > +
>> >> >> >>> >>> > def test_r2eff_read(self):
>> >> >> >>> >>> > """Test the operation of the
>> >> >> >>> >>> > relax_disp.r2eff_read
>> >> >> >>> >>> > user
>> >> >> >>> >>> > function."""
>> >> >> >>> >>> >
>> >> >> >>> >>> >
>> >> >> >>> >>> >
>> >> >> >>> >>> > _______________________________________________
>> >> >> >>> >>> > relax (http://www.nmr-relax.com)
>> >> >> >>> >>> >
>> >> >> >>> >>> > This is the relax-commits mailing list
>> >> >> >>> >>> > relax-commits@xxxxxxx
>> >> >> >>> >>> >
>> >> >> >>> >>> > 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
>> >> >> >>> >>> relax-devel@xxxxxxx
>> >> >> >>> >>>
>> >> >> >>> >>>
>> >> >> >>> >>> 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
>> >> >> >>> >>
>> >> >> >>> >>
>> >> >> >>
>> >> >> >>
>> >> >> >
>> >> >
>> >> >
>> >
>> >
>
>