Author: tlinnet
Date: Fri Jun 20 08:11:53 2014
New Revision: 24178
URL: http://svn.gna.org/viewcvs/relax?rev=24178&view=rev
Log:
Added the systemtest: test_cpmg_synthetic_b14_to_ns_star_cluster, to check
for the model is still working after change.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
Modified:
branches/disp_spin_speed/test_suite/system_tests/relax_disp.py
Modified: branches/disp_spin_speed/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/system_tests/relax_disp.py?rev=24178&r1=24177&r2=24178&view=diff
==============================================================================
--- branches/disp_spin_speed/test_suite/system_tests/relax_disp.py
(original)
+++ branches/disp_spin_speed/test_suite/system_tests/relax_disp.py Fri
Jun 20 08:11:53 2014
@@ -1201,6 +1201,152 @@
model_create = 'B14'
#model_create = 'NS CPMG 2-site expanded'
model_analyse = 'NS CPMG 2-site 3D'
+
+ # 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_errs_1 = [0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05]
+ r2eff_errs_1 = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+ exp_1 = [sfrq_1, time_T2_1, ncycs_1, r2eff_errs_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_errs_2 = [0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05]
+ r2eff_errs_2 = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+ exp_2 = [sfrq_2, time_T2_2, ncycs_2, r2eff_errs_2]
+
+ # Collect all exps
+ exps = [exp_1, exp_2]
+
+ spins = [
+ ['Ala', 1, 'N', {'r2': {r20_key_1:10., r20_key_2:11.5}, 'r2a':
{r20_key_1:10., r20_key_2:11.5}, 'r2b': {r20_key_1:10., r20_key_2:11.5},
'kex': 1000., 'pA': 0.95, 'dw': 2.} ],
+ ['Ala', 2, 'N', {'r2': {r20_key_1:13., r20_key_2:14.5}, 'r2a':
{r20_key_1:13., r20_key_2:14.5}, 'r2b': {r20_key_1:13., r20_key_2:14.5},
'kex': 1000., 'pA': 0.95, 'dw': 1.} ]
+ ]
+
+ # 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 r20_from_min_r2eff ?.
+ ds.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 = True
+
+ # 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-8
+
+ # The maximum number of iterations.
+ # The default value is 1e7.
+ ds.set_max_iter = 10000
+
+ # 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 = True
+
+ # 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]
+
+ # Extract the clust results.
+ min_params = ds.clust_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, 1)
+ 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, 1)
+ elif mo_param == 'kex':
+ self.assertAlmostEqual(set_val/1000, min_val/1000, 1)
+ elif mo_param == 'pA':
+ self.assertAlmostEqual(set_val, min_val, 2)
+
+
+ def test_cpmg_synthetic_b14_to_ns_star_cluster(self):
+ """Test synthetic cpmg data. Created with B14, analysed with NS
CPMG 2site STAR, for clustered analysis.
+
+ This is part of: U{Task #7807
<https://gna.org/task/index.php?7807>}: Speed-up of dispersion models for
Clustered analysis.
+
+ This script will produce synthetic CPMG R2eff values according to
the selected model, and the fit the selected model.
+ """
+
+ # Reset.
+ #self.interpreter.reset()
+
+ ## Set Experiments.
+ model_create = 'B14'
+ #model_create = 'NS CPMG 2-site expanded'
+ model_analyse = 'NS CPMG 2-site star'
# Exp 1
sfrq_1 = 599.8908617*1E6
r24178 - /branches/disp_spin_speed/test_suite/system_tests/relax_disp.py