Author: tlinnet
Date: Mon Aug 25 01:50:58 2014
New Revision: 25239
URL: http://svn.gna.org/viewcvs/relax?rev=25239&view=rev
Log:
Added systemtest Relax_disp.test_estimate_r2eff_error().
This is to get insight in the error difference between 2000 monto carlo
simulations and then scipy.optimize.leastsq.
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 431.0.
r2eff=8.646/8.646 r2eff_err=0.0348/0.0692 i0=202664.191/202664.191
i0_err=699.6443/712.4201
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 651.2.
r2eff=10.377/10.377 r2eff_err=0.0403/0.0810 i0=206049.558/206049.558
i0_err=776.4215/782.1833
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 800.5.
r2eff=10.506/10.506 r2eff_err=0.0440/0.0853 i0=202586.332/202586.332
i0_err=763.9678/758.7052
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 984.0.
r2eff=10.903/10.903 r2eff_err=0.0476/0.0922 i0=203455.021/203455.021
i0_err=837.8779/828.7280
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 1341.1.
r2eff=10.684/10.684 r2eff_err=0.0446/0.0853 i0=218670.412/218670.411
i0_err=850.0210/830.9558
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 1648.5.
r2eff=10.501/10.501 r2eff_err=0.0371/0.0742 i0=206502.512/206502.512
i0_err=794.0523/772.9843
R1rho at 799.8 MHz, for offset=124.247 ppm and dispersion point 1341.1.
r2eff=11.118/11.118 r2eff_err=0.0413/0.0827 i0=216447.241/216447.241
i0_err=784.6562/788.0384
R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 800.5.
r2eff=7.866/7.866 r2eff_err=0.0347/0.0695 i0=211869.715/211869.715
i0_err=749.2776/763.6930
R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 1341.1.
r2eff=9.259/9.259 r2eff_err=0.0331/0.0661 i0=217703.151/217703.151
i0_err=682.2137/685.5838
R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 1648.5.
r2eff=9.565/9.565 r2eff_err=0.0373/0.0745 i0=211988.939/211988.939
i0_err=839.0313/827.0373
R1rho at 799.8 MHz, for offset=142.754 ppm and dispersion point 800.5.
r2eff=3.240/3.240 r2eff_err=0.0127/0.0253 i0=214417.382/214417.382
i0_err=595.8865/613.4378
R1rho at 799.8 MHz, for offset=142.754 ppm and dispersion point 1341.1.
r2eff=5.084/5.084 r2eff_err=0.0177/0.0352 i0=226358.691/226358.691
i0_err=660.5314/655.7670
R1rho at 799.8 MHz, for offset=179.768 ppm and dispersion point 1341.1.
r2eff=2.208/2.208 r2eff_err=0.0091/0.0178 i0=228620.553/228620.553
i0_err=564.8353/560.0873
R1rho at 799.8 MHz, for offset=241.459 ppm and dispersion point 1341.1.
r2eff=1.711/1.711 r2eff_err=0.0077/0.0155 i0=224087.486/224087.486
i0_err=539.4300/546.4217
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
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=25239&r1=25238&r2=25239&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Mon Aug 25 01:50:58 2014
@@ -2726,6 +2726,94 @@
# Verify the data.
self.verify_r1rho_kjaergaard_missing_r1(models=MODELS,
result_dir_name=result_dir_name, do_assert=False)
+
+
+ def test_estimate_r2eff_error(self):
+ """Test the user function for estimating R2eff and associated errors
for exponential curve fitting.
+ This is compared with a run where erros are estimated by 2000 Monte
Carlo simulations.
+
+ This follows Task 7822.
+ U{task #7822<https://gna.org/task/index.php?7822>}: Implement user
function to estimate R2eff and associated errors for exponential curve
fitting.
+
+ This uses the data from Kjaergaard's paper at U{DOI:
10.1021/bi4001062<http://dx.doi.org/10.1021/bi4001062>}.
+ Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho
relaxation dispersion experiments using the 'DPL' model.
+ """
+
+ # Define data path.
+ prev_data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013'
+sep+ "check_graphs" +sep+ "mc_2000" +sep+ "R2eff"
+
+ # Create pipe.
+ self.interpreter.pipe.create('MC_2000', 'relax_disp')
+
+ # Read results for 2000 MC simulations.
+ self.interpreter.results.read(prev_data_path + sep + 'results')
+
+ # Start dic.
+ my_dic = {}
+ param_key_list = []
+
+ for cur_spin, mol_name, resi, resn, spin_id in
spin_loop(full_info=True, return_id=True, skip_desel=True):
+ # Add key to dic.
+ my_dic[spin_id] = {}
+
+ # Generate spin string.
+ spin_string = generate_spin_string(spin=cur_spin,
mol_name=mol_name, res_num=resi, res_name=resn)
+
+ for exp_type, frq, offset, point, ei, mi, oi, di in
loop_exp_frq_offset_point(return_indices=True):
+ # Generate the param_key.
+ param_key = return_param_key_from_data(exp_type=exp_type,
frq=frq, offset=offset, point=point)
+
+ # Append key.
+ param_key_list.append(param_key)
+
+ # Add key to dic.
+ my_dic[spin_id][param_key] = {}
+
+ # Get the value.
+ r2eff = getattr(cur_spin, 'r2eff')[param_key]
+ r2eff_err = getattr(cur_spin, 'r2eff_err')[param_key]
+ i0 = getattr(cur_spin, 'i0')[param_key]
+ i0_err = getattr(cur_spin, 'i0_err')[param_key]
+
+ # Save to dic.
+ my_dic[spin_id][param_key]['r2eff'] = r2eff
+ my_dic[spin_id][param_key]['r2eff_err'] = r2eff_err
+ my_dic[spin_id][param_key]['i0'] = i0
+ my_dic[spin_id][param_key]['i0_err'] = i0_err
+
+ # A new data pipe.
+ self.interpreter.pipe.copy(pipe_from='MC_2000', pipe_to='r2eff_est')
+ self.interpreter.pipe.switch(pipe_name='r2eff_est')
+
+ # Set the model.
+ self.interpreter.relax_disp.select_model(MODEL_R2EFF)
+
+ # Estimate R2eff and errors.
+ self.interpreter.relax_disp.r2eff_estimate(verbosity=0)
+
+ for cur_spin, mol_name, resi, resn, spin_id in
spin_loop(full_info=True, return_id=True, skip_desel=True):
+ # Generate spin string.
+ spin_string = generate_spin_string(spin=cur_spin,
mol_name=mol_name, res_num=resi, res_name=resn)
+
+ for exp_type, frq, offset, point, ei, mi, oi, di in
loop_exp_frq_offset_point(return_indices=True):
+ # Generate the param_key.
+ param_key = return_param_key_from_data(exp_type=exp_type,
frq=frq, offset=offset, point=point)
+
+ # Get the value.
+ r2eff_est = getattr(cur_spin, 'r2eff')[param_key]
+ r2eff_err_est = getattr(cur_spin, 'r2eff_err')[param_key]
+ i0_est = getattr(cur_spin, 'i0')[param_key]
+ i0_err_est = getattr(cur_spin, 'i0_err')[param_key]
+
+ # Get from dic.
+ r2eff = my_dic[spin_id][param_key]['r2eff']
+ r2eff_err = my_dic[spin_id][param_key]['r2eff_err']
+ i0 = my_dic[spin_id][param_key]['i0']
+ i0_err = my_dic[spin_id][param_key]['i0_err']
+
+ print("%s at %3.1f MHz, for offset=%3.3f ppm and dispersion
point %-5.1f." % (exp_type, frq/1E6, offset, point) )
+ print("r2eff=%3.3f/%3.3f r2eff_err=%3.4f/%3.4f" % (r2eff,
r2eff_est, r2eff_err, r2eff_err_est) ),
+ print("i0=%3.3f/%3.3f i0_err=%3.4f/%3.4f\n" % (i0, i0_est,
i0_err, i0_err_est) )
def test_exp_fit(self):
r25239 - /trunk/test_suite/system_tests/relax_disp.py