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 <tlinnet@xxxxxxxxxxxxx>:
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):
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Re: r22198 - /trunk/test_suite/system_tests/relax_disp.py