Author: tlinnet
Date: Sun Aug 31 16:55:09 2014
New Revision: 25484
URL: http://svn.gna.org/viewcvs/relax?rev=25484&view=rev
Log:
Inserted possibility for boot-strapping in systemtest
Relax_disp.test_estimate_r2eff_err_methods.
This shows, that the boot strapping method get the SAME estimation for R2eff
errors, as the estimate_r2eff_err() function!
This must either mean, that the OLD Monte-Carlo simulation was corrupted, or
the creation of data in Monte-Carlo simulations is corrupted.
For the r2eff columns.
0.0348/0.0692/0.0348/0.0691
Old MC 2000/Estimated from Co-var/Manual re-calc of old MC/ Boot strapping
2000 simulations.
-------------
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 431.0.
r2eff=8.646/8.646 r2eff_err=0.0348/0.0692/0.0348/0.0691
i0=202664.191/202664.191 i0_err=699.6443/712.4201/699.6443/693.1613
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 651.2.
r2eff=10.377/10.377 r2eff_err=0.0403/0.0810/0.0403/0.0823
i0=206049.558/206049.558 i0_err=776.4215/782.1833/776.4215/763.6342
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 800.5.
r2eff=10.506/10.506 r2eff_err=0.0440/0.0853/0.0440/0.0887
i0=202586.332/202586.332 i0_err=763.9678/758.7052/763.9678/776.2788
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 984.0.
r2eff=10.903/10.903 r2eff_err=0.0476/0.0922/0.0476/0.0968
i0=203455.021/203455.021 i0_err=837.8779/828.7280/837.8779/834.3398
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 1341.1.
r2eff=10.684/10.684 r2eff_err=0.0446/0.0853/0.0446/0.0889
i0=218670.412/218670.412 i0_err=850.0210/830.9558/850.0210/825.7990
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 1648.5.
r2eff=10.501/10.501 r2eff_err=0.0371/0.0742/0.0371/0.0754
i0=206502.512/206502.512 i0_err=794.0523/772.9843/794.0523/776.3687
R1rho at 799.8 MHz, for offset=124.247 ppm and dispersion point 1341.1.
r2eff=11.118/11.118 r2eff_err=0.0413/0.0827/0.0413/0.0870
i0=216447.241/216447.241 i0_err=784.6562/788.0384/784.6562/810.1911
R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 800.5.
r2eff=7.866/7.866 r2eff_err=0.0347/0.0695/0.0347/0.0712
i0=211869.715/211869.715 i0_err=749.2776/763.6930/749.2776/747.9741
R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 1341.1.
r2eff=9.259/9.259 r2eff_err=0.0331/0.0661/0.0331/0.0680
i0=217703.151/217703.151 i0_err=682.2137/685.5838/682.2137/700.1831
R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 1648.5.
r2eff=9.565/9.565 r2eff_err=0.0373/0.0745/0.0373/0.0743
i0=211988.939/211988.939 i0_err=839.0313/827.0373/839.0313/815.4495
R1rho at 799.8 MHz, for offset=142.754 ppm and dispersion point 800.5.
r2eff=3.240/3.240 r2eff_err=0.0127/0.0253/0.0127/0.0254
i0=214417.382/214417.382 i0_err=595.8865/613.4378/595.8865/606.4650
R1rho at 799.8 MHz, for offset=142.754 ppm and dispersion point 1341.1.
r2eff=5.084/5.084 r2eff_err=0.0177/0.0352/0.0177/0.0353
i0=226358.691/226358.691 i0_err=660.5314/655.7670/660.5314/666.9979
R1rho at 799.8 MHz, for offset=179.768 ppm and dispersion point 1341.1.
r2eff=2.208/2.208 r2eff_err=0.0091/0.0178/0.0091/0.0176
i0=228620.553/228620.553 i0_err=564.8353/560.0873/564.8353/558.6988
R1rho at 799.8 MHz, for offset=241.459 ppm and dispersion point 1341.1.
r2eff=1.711/1.711 r2eff_err=0.0077/0.0155/0.0077/0.0158
i0=224087.486/224087.486 i0_err=539.4300/546.4217/539.4300/556.5093
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=25484&r1=25483&r2=25484&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Sun Aug 31 16:55:09 2014
@@ -3122,6 +3122,16 @@
my_dic = {}
param_key_list = []
+ # Do boot strapping ?
+ do_boot = True
+ if do_boot:
+ from minfx.generic import generic_minimise
+ from random import gauss
+ min_algor = 'BFGS'
+ min_options = ()
+ sim_boot = 2000
+ scaling_list = [1.0, 1.0]
+
# First check sim values.
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.
@@ -3190,6 +3200,50 @@
self.assertAlmostEqual(r2eff_sim_err, r2eff_err)
self.assertAlmostEqual(i0_sim_err, i0_err)
+ if do_boot:
+ values = []
+ errors = []
+ times = []
+ for time in loop_time(exp_type=exp_type, frq=frq,
offset=offset, point=point):
+ values.append(average_intensity(spin=cur_spin,
exp_type=exp_type, frq=frq, offset=offset, point=point, time=time))
+ errors.append(average_intensity(spin=cur_spin,
exp_type=exp_type, frq=frq, offset=offset, point=point, time=time,
error=True))
+ times.append(time)
+
+ # Convert to numpy array.
+ values = asarray(values)
+ errors = asarray(errors)
+ times = asarray(times)
+
+ R_m_sim_l = []
+ I0_m_sim_l = []
+ for j in range(sim_boot):
+ if j in range(0, 100000, 100):
+ print("Simulation %i"%j)
+ # Start minimisation.
+
+ # Produce errors
+ I_err = []
+ for j, error in enumerate(errors):
+ I_error = gauss(values[j], error)
+ I_err.append(I_error)
+ # Convert to numpy array.
+ I_err = asarray(I_err)
+
+ x0 = [r2eff, i0]
+ setup(num_params=len(x0), num_times=len(times),
values=I_err, sd=errors, relax_times=times, scaling_matrix=scaling_list)
+
+ params_minfx_sim_j, chi2_minfx_sim_j, iter_count,
f_count, g_count, h_count, warning = generic_minimise(func=func, dfunc=dfunc,
args=(), x0=x0, min_algor=min_algor, min_options=min_options,
full_output=True, print_flag=0)
+ R_m_sim_j, I0_m_sim_j = params_minfx_sim_j
+ R_m_sim_l.append(R_m_sim_j)
+ I0_m_sim_l.append(I0_m_sim_j)
+
+ # Get stats on distribution.
+ sigma_R_sim = std(asarray(R_m_sim_l), ddof=1)
+ sigma_I0_sim = std(asarray(I0_m_sim_l), ddof=1)
+ my_dic[spin_id][param_key]['r2eff_err_boot'] =
sigma_R_sim
+ my_dic[spin_id][param_key]['i0_err_boot'] = sigma_I0_sim
+
+
# A new data pipe.
self.interpreter.pipe.copy(pipe_from='MC_2000', pipe_to='r2eff_est')
self.interpreter.pipe.switch(pipe_name='r2eff_est')
@@ -3227,9 +3281,16 @@
r2eff_sim_err = my_dic[spin_id][param_key]['r2eff_err_sim']
i0_sim_err = my_dic[spin_id][param_key]['i0_err_sim']
+ if do_boot:
+ r2eff_boot_err =
my_dic[spin_id][param_key]['r2eff_err_boot']
+ i0_boot_err = my_dic[spin_id][param_key]['i0_err_boot']
+ else:
+ r2eff_boot_err = 0.0
+ i0_boot_err = 0.0
+
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/%3.4f" %
(r2eff, r2eff_est, r2eff_err, r2eff_err_est, r2eff_sim_err) ),
- print("i0=%3.3f/%3.3f i0_err=%3.4f/%3.4f/%3.4f\n" % (i0,
i0_est, i0_err, i0_err_est, i0_sim_err) )
+ print("r2eff=%3.3f/%3.3f r2eff_err=%3.4f/%3.4f/%3.4f/%3.4f"
% (r2eff, r2eff_est, r2eff_err, r2eff_err_est, r2eff_sim_err, r2eff_boot_err)
),
+ print("i0=%3.3f/%3.3f i0_err=%3.4f/%3.4f/%3.4f/%3.4f\n" %
(i0, i0_est, i0_err, i0_err_est, i0_sim_err, i0_boot_err) )
# Now do it manually.
r25484 - /trunk/test_suite/system_tests/relax_disp.py