Author: tlinnet
Date: Wed May 21 20:36:33 2014
New Revision: 23315
URL: http://svn.gna.org/viewcvs/relax?rev=23315&view=rev
Log:
Implemented systemtest Relax_disp.test_cpmg_synthetic_ns3d_to_b14.
bug #22021: (https://gna.org/bugs/?22021) Model B14 shows bad fitting to
data.
This is to catch model B14 showing bad fitting behaviour.
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=23315&r1=23314&r2=23315&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Wed May 21 20:36:33 2014
@@ -1091,6 +1091,145 @@
self.assertAlmostEqual(set_val/1000,
min_val/1000, 1)
elif mo_param == 'pA':
self.assertAlmostEqual(set_val, min_val, 3)
+
+
+ def test_cpmg_synthetic_ns3d_to_b14(self):
+ """Test synthetic cpmg data.
+
+ This script will produce synthetic CPMG R2eff values according to
the NS CPMG 2-site 3D model, and the fit the data with B14.
+ Try to catch bug #22021 U{https://gna.org/bugs/index.php?22021}:
Model B14 shows bad fitting to data.
+ """
+
+ # Reset.
+ #self.interpreter.reset()
+
+ ## Set Experiments.
+ model_create = 'NS CPMG 2-site 3D'
+ #model_create = 'NS CPMG 2-site expanded'
+ model_analyse = 'B14'
+ # Exp 1
+ sfrq_1 = 599.8908617*1E6
+ r20_key_1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ,
frq=sfrq_1)
+ time_T2_1 = 0.06
+ ncycs_1 = [2, 4, 8, 10, 20, 30, 40, 60]
+ r2eff_err_1 = [0, 0, 0, 0, 0, 0, 0, 0]
+ exp_1 = [sfrq_1, time_T2_1, ncycs_1, r2eff_err_1]
+
+ sfrq_2 = 499.8908617*1E6
+ r20_key_2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ,
frq=sfrq_2)
+ time_T2_2 = 0.05
+ ncycs_2 = [2, 4, 8, 10, 30, 35, 40, 50]
+ r2eff_err_2 = [0, 0, 0, 0, 0, 0, 0, 0]
+ exp_2 = [sfrq_2, time_T2_2, ncycs_2, r2eff_err_2]
+
+ # Collect all exps
+ exps = [exp_1, exp_2]
+
+ spins = [
+ ['Ala', 1, 'N', {'r2': {r20_key_1:10., r20_key_2:10.}, 'r2a':
{r20_key_1:10., r20_key_2:10.}, 'r2b': {r20_key_1:10., r20_key_2:10.},
'kex': 1000., 'pA': 0.99, 'dw': 2.} ]
+ ]
+
+ # Collect the data to be used.
+ ds.data = [model_create, model_analyse, spins, exps]
+
+ # The tmp directory. None is the local directory.
+ ds.tmpdir = ds.tmpdir
+
+ # The results directory. None is the local directory.
+ #ds.resdir = None
+ ds.resdir = ds.tmpdir
+
+ # Do set_grid_r20_from_min_r2eff ?.
+ ds.set_grid_r20_from_min_r2eff = True
+
+ # Remove insignificant level.
+ ds.insignificance = 0.0
+
+ # The grid search size (the number of increments per dimension).
+ ds.GRID_INC = 8
+
+ # The do clustering.
+ ds.do_cluster = False
+
+ # The function tolerance. This is used to terminate minimisation
once the function value between iterations is less than the tolerance.
+ # The default value is 1e-25.
+ ds.set_func_tol = 1e-9
+
+ # The maximum number of iterations.
+ # The default value is 1e7.
+ ds.set_max_iter = 1000
+
+ # The verbosity level.
+ ds.verbosity = 1
+
+ # The rel_change WARNING level.
+ ds.rel_change = 0.05
+
+ # The plot_curves.
+ ds.plot_curves = False
+
+ # The conversion for ShereKhan at http://sherekhan.bionmr.org/.
+ ds.sherekhan_input = False
+
+ # Make a dx map to be opened om OpenDX. To map the hypersurface
of chi2, when altering kex, dw and pA.
+ ds.opendx = False
+
+ # The set r2eff err.
+ ds.r2eff_err = 0.1
+
+ # The print result info.
+ ds.print_res = False
+
+ # Execute the script.
+ self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'cpmg_synthetic.py')
+
+ cur_spins = ds.data[2]
+ # Compare results.
+ for i in range(len(cur_spins)):
+ res_name, res_num, spin_name, params = cur_spins[i]
+ cur_spin_id = ":%i@%s"%(res_num, spin_name)
+ cur_spin = return_spin(cur_spin_id)
+
+ grid_params = ds.grid_results[i][3]
+ min_params = ds.min_results[i][3]
+ # Now read the parameters.
+ print("For spin: '%s'"%cur_spin_id)
+ for mo_param in cur_spin.params:
+ # The R2 is a dictionary, depending on spectrometer
frequency.
+ if isinstance(getattr(cur_spin, mo_param), dict):
+ grid_r2 = grid_params[mo_param]
+ min_r2 = min_params[mo_param]
+ set_r2 = params[mo_param]
+ for key, val in set_r2.items():
+ grid_r2_frq = grid_r2[key]
+ min_r2_frq = min_r2[key]
+ set_r2_frq = set_r2[key]
+ frq = float(key.split(EXP_TYPE_CPMG_SQ+' -
')[-1].split('MHz')[0])
+ rel_change = math.sqrt( (min_r2_frq -
set_r2_frq)**2/(min_r2_frq)**2 )
+ print("%s %s %s %s %.1f GRID=%.3f MIN=%.3f
SET=%.3f RELC=%.3f"%(cur_spin.model, res_name, cur_spin_id, mo_param, frq,
grid_r2_frq, min_r2_frq, set_r2_frq, rel_change) )
+ if rel_change > ds.rel_change:
+ print("WARNING: rel change level is above
%.2f, and is %.4f."%(ds.rel_change, rel_change))
+ print("###################################")
+
+ ## Make test on R2.
+ self.assertAlmostEqual(set_r2_frq, min_r2_frq, 2)
+ else:
+ grid_val = grid_params[mo_param]
+ min_val = min_params[mo_param]
+ set_val = params[mo_param]
+ rel_change = math.sqrt( (min_val -
set_val)**2/(min_val)**2 )
+ print("%s %s %s %s GRID=%.3f MIN=%.3f SET=%.3f
RELC=%.3f"%(cur_spin.model, res_name, cur_spin_id, mo_param, grid_val,
min_val, set_val, rel_change) )
+ if rel_change > ds.rel_change:
+ print("WARNING: rel change level is above %.2f,
and is %.4f."%(ds.rel_change, rel_change))
+ print("###################################")
+
+ ## Make test on parameters.
+ if mo_param == 'dw':
+ self.assertAlmostEqual(set_val/10, min_val/10, 6)
+ elif mo_param == 'kex':
+ self.assertAlmostEqual(set_val/1000,
min_val/1000, 5)
+ elif mo_param == 'pA':
+ self.assertAlmostEqual(set_val, min_val, 7)
def test_cpmg_synthetic_ns3d_to_cr72_noise_cluster(self):
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Re: r23315 - /trunk/test_suite/system_tests/relax_disp.py