Re: r25777 - /trunk/test_suite/system_tests/relax_fit.py -- September 12, 2014 - 12:08

Hi Troels,

If you were to change the line:

+            self.interpreter.relax_fit.rx_err_estimate()

to:

+            self.interpreter.error_analysis.covariance_matrix()

that would be the perfect system test for the steps I mentioned at
http://thread.gmane.org/gmane.science.nmr.relax.scm/23526/focus=7096.

Cheers,

Edward



On 12 September 2014 11:25,  <tlinnet@xxxxxxxxxxxxx> wrote:
> Author: tlinnet
> Date: Fri Sep 12 11:25:58 2014
> New Revision: 25777
>
> URL: http://svn.gna.org/viewcvs/relax?rev=25777&view=rev
> Log:
> Extended systemtest Relax_fit.test_curve_fitting_height_estimate_error() to 
> test the error estimation method from the Co-variance matrix.
>
> The results seems very similar, if increasing to 2000 Monte-Carlo 
> simulations.
>
> Modified:
>     trunk/test_suite/system_tests/relax_fit.py
>
> Modified: trunk/test_suite/system_tests/relax_fit.py
> URL: 
> http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_fit.py?rev=25777&r1=25776&r2=25777&view=diff
> ==============================================================================
> --- trunk/test_suite/system_tests/relax_fit.py  (original)
> +++ trunk/test_suite/system_tests/relax_fit.py  Fri Sep 12 11:25:58 2014
> @@ -376,6 +376,70 @@
>          # Check the curve-fitting results.
>          self.check_curve_fitting_manual()
>
> +        # Compare rx errors.
> +        if True:
> +            # Estimate rx and i0 errors.
> +            self.interpreter.relax_fit.rx_err_estimate()
> +
> +            # Collect:
> +            i0_est = []
> +            i0_err_est = []
> +            rx_est = []
> +            rx_err_est = []
> +            for cur_spin, mol_name, resi, resn, spin_id in 
> spin_loop(full_info=True, return_id=True, skip_desel=True):
> +                i0_est.append(cur_spin.i0)
> +                i0_err_est.append(cur_spin.i0_err)
> +                rx_est.append(cur_spin.rx)
> +                rx_err_est.append(cur_spin.rx_err)
> +
> +            # Set number of MC simulati0ns
> +            MC_SIM = 200
> +
> +            # Monte Carlo simulations.
> +            self.interpreter.monte_carlo.setup(number=MC_SIM)
> +            self.interpreter.monte_carlo.create_data()
> +            self.interpreter.monte_carlo.initial_values()
> +            self.interpreter.minimise.execute(min_method, scaling=False, 
> constraints=False)
> +            self.interpreter.monte_carlo.error_analysis()
> +
> +            # Collect:
> +            i0_mc = []
> +            i0_err_mc = []
> +            rx_mc = []
> +            rx_err_mc = []
> +            for cur_spin, mol_name, resi, resn, spin_id in 
> spin_loop(full_info=True, return_id=True, skip_desel=True):
> +                i0_mc.append(cur_spin.i0)
> +                i0_err_mc.append(cur_spin.i0_err)
> +                rx_mc.append(cur_spin.rx)
> +                rx_err_mc.append(cur_spin.rx_err)
> +
> +            # Now print and compare
> +            i = 0
> +            print("Comparison between error estimation from Jacobian 
> co-variance matrix and Monte-Carlo simulations.")
> +            print("Spin ID: rx_err_diff=est-MC, i0_err_diff=est-MC, 
> rx_err=est/MC, i0_err=est/MC, i0=est/MC, rx=est/MC.")
> +            for cur_spin, mol_name, resi, resn, spin_id in 
> spin_loop(full_info=True, return_id=True, skip_desel=True):
> +                # Extract for estimation.
> +                i0_est_i = i0_est[i]
> +                i0_err_est_i = i0_err_est[i]
> +                rx_est_i = rx_est[i]
> +                rx_err_est_i = rx_err_est[i]
> +
> +                # Extract from monte carlo.
> +                i0_mc_i = i0_mc[i]
> +                i0_err_mc_i = i0_err_mc[i]
> +                rx_mc_i = rx_mc[i]
> +                rx_err_mc_i = rx_err_mc[i]
> +
> +                # Add to counter.
> +                i += 1
> +
> +                # Prepare text.
> +                rx_err_diff = rx_err_est_i - rx_err_mc_i
> +                i0_err_diff = i0_err_est_i - i0_err_mc_i
> +
> +                text = "Spin '%s': rx_err_diff=%3.4f, i0_err_diff=%3.3f, 
> rx_err=%3.4f/%3.4f, i0_err=%3.3f/%3.3f, rx=%3.3f/%3.3f, i0=%3.3f/%3.3f" % 
> (spin_id, rx_err_diff, i0_err_diff, rx_err_est_i, rx_err_mc_i, 
> i0_err_est_i, i0_err_mc_i, rx_est_i, rx_mc_i, i0_est_i, i0_mc_i)
> +                print(text)
> +
>
>      def test_curve_fitting_volume(self):
>          """Test the relaxation curve fitting C modules."""
>
>
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