Hi Edward.
I just added this system test:
relax -s Relax_disp.test_cpmg_synthetic_cr72_fail -d
I am quite concerned about this.
It proves that small R2eff errors of 0.05, will make the minimisation
go terrible wrong.
For a spin with dw=2, it goes okay, but with dw=1, it finds pA=0.5
instead of 0.99.
For spin: ':1@N'
CR72 Ala :1@N r2 599.9 GRID=10.067 MIN=9.985 SET=10.000 RELC=0.002
CR72 Ala :1@N r2 499.9 GRID=11.531 MIN=11.496 SET=11.500 RELC=0.000
CR72 Ala :1@N pA GRID=0.955 MIN=0.989 SET=0.990 RELC=0.001
CR72 Ala :1@N dw GRID=0.909 MIN=1.931 SET=2.000 RELC=0.036
CR72 Ala :1@N kex GRID=1819.000 MIN=1027.289 SET=1000.000 RELC=0.027
For spin: ':2@N'
CR72 Ala :2@N r2 599.9 GRID=12.979 MIN=13.073 SET=13.000 RELC=0.006
CR72 Ala :2@N r2 499.9 GRID=14.470 MIN=14.477 SET=14.500 RELC=0.002
CR72 Ala :2@N pA GRID=0.500 MIN=0.500 SET=0.990 RELC=0.980
WARNING: rel change level is above 0.05, and is 0.9800.
###################################
CR72 Ala :2@N dw GRID=6.364 MIN=3.505 SET=1.000 RELC=0.715
WARNING: rel change level is above 0.05, and is 0.7147.
###################################
CR72 Ala :2@N kex GRID=1.000 MIN=1.885 SET=1000.000 RELC=529.556
WARNING: rel change level is above 0.05, and is 529.5564.
###################################
Try also this, to get the graphs in a test folder.
relax test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py
This really looks like my problem for my SOD1 WT dataset.
We think that all of the dw values are 2x to big.
So, I am quite suspicious for the minimisation of dw values.
Ughhh....
Best
Troels
---------- Forwarded message ----------
From: <tlinnet@xxxxxxxxxxxxx>
Date: 2014-05-02 14:47 GMT+02:00
Subject: r22933 - /trunk/test_suite/system_tests/relax_disp.py
To: relax-commits@xxxxxxx
Author: tlinnet
Date: Fri May 2 14:47:19 2014
New Revision: 22933
URL: http://svn.gna.org/viewcvs/relax?rev=22933&view=rev
Log:
Added a systemtest, which proves that small dw values of 1, makes the
mimisation goes wrong.
This is for synthetic data with R2eff values of +/- 0.05, which is to
be expected for real data.
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=22933&r1=22932&r2=22933&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Fri May 2 14:47:19 2014
@@ -760,6 +760,129 @@
## Make test on parameters.
self.assertAlmostEqual(set_val, min_val, 10)
+
+
+ def test_cpmg_synthetic_cr72_fail(self):
+ """Test synthetic cpmg data. Make CR72 model fail, for small noise.
+
+ 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 = "CR72"
+ # 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 = [0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05]
+ 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 = [0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05]
+ 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_2:11.5},
'kex': 1000, 'pA': 0.99, 'dw': 2} ],
+ ['Ala', 2, 'N', {'r2': {r20_key_1:13, r20_key_2:14.5},
'kex': 1000, 'pA': 0.99, 'dw': 1} ]
+ ]
+
+ # Collect the data to be used.
+ ds.data = [model, 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 = 11
+
+ # 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-15
+
+ # The maximum number of iterations.
+ # The default value is 1e7.
+ ds.set_max_iter = 1000000
+
+ # The verbosity level.
+ ds.verbosity = 1
+
+ # The rel_change WARNING level.
+ ds.rel_change = 0.05
+
+ # The plot_curves.
+ ds.plot_curves = 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[1]
+ # 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/10, min_r2_frq/10,
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.
+ self.assertAlmostEqual(set_val, min_val, 1)
def test_curve_type_cpmg_fixed_time(self):
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Fwd: r22933 - /trunk/test_suite/system_tests/relax_disp.py