This is a good idea. Note that setting the MC sim number to -1 is only possible in a script, and not the GUI. Oh, you changed that later. An alternative would be to add the curve_fit_errors argument which defaults to 'MC' but can be set to 'covar'. I would suggest also having a RelaxWarning in the auto-analysis about the covariance matrix being of lower accuracy than MC sims, just so the user is more aware.
Cheers, Edward On 27 August 2014 21:55, <[email protected]> wrote: > Author: tlinnet > Date: Wed Aug 27 21:55:19 2014 > New Revision: 25358 > > URL: http://svn.gna.org/viewcvs/relax?rev=25358&view=rev > Log: > Added systemtest, Relax_disp.test_estimate_r2eff_err_auto and extended > functionality to the auto analyses protocol. > > If "exp_mc_sim_num" is set to "-1" and sent to the auto analyses, the errors > of R2eff will be estimated from the Co-Variance matrix. > > These errors is HIGHLY likely to be wrong, but can be used in an initial test > fase, to rapidly produce data for plotting data. > > task #7822(https://gna.org/task/index.php?7822): Implement user function to > estimate R2eff and associated errors for exponential curve fitting. > > Modified: > trunk/auto_analyses/relax_disp.py > trunk/test_suite/system_tests/relax_disp.py > > Modified: trunk/auto_analyses/relax_disp.py > URL: > http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/relax_disp.py?rev=25358&r1=25357&r2=25358&view=diff > ============================================================================== > --- trunk/auto_analyses/relax_disp.py (original) > +++ trunk/auto_analyses/relax_disp.py Wed Aug 27 21:55:19 2014 > @@ -497,18 +497,31 @@ > # The minimisation algorithm to use. If the Jacobian and Hessian > matrix have not been specified for fitting, 'simplex' should be used. > min_algor = 'simplex' > > - # Do Monte Carlo simulations. > + # Error estimation by Monte Carlo simulations. > if do_monte_carlo: > + # Set the number of Monte-Carlo simulations. > + monte_carlo_sim = self.mc_sim_num > + > + # If the number for exponential curve fitting has been set. > if model == MODEL_R2EFF and self.exp_mc_sim_num != None: > - > self.interpreter.monte_carlo.setup(number=self.exp_mc_sim_num) > + monte_carlo_sim = self.exp_mc_sim_num > + > + # When set to minus 1, estimation of the errors will be > extracted from the covariance matrix. > + # This is HIGHLY likely to be wrong, but can be used in an > initial test fase. > + if model == MODEL_R2EFF and self.exp_mc_sim_num == -1: > + # Print > + subsection(file=sys.stdout, text="Estimating errors from > Covariance matrix", prespace=1) > + > + # Estimate errors > + self.interpreter.relax_disp.r2eff_err_estimate() > else: > - self.interpreter.monte_carlo.setup(number=self.mc_sim_num) > - self.interpreter.monte_carlo.create_data() > - self.interpreter.monte_carlo.initial_values() > - self.interpreter.minimise.execute(min_algor=min_algor, > func_tol=self.opt_func_tol, max_iter=self.opt_max_iterations, > constraints=constraints) > - if self.eliminate: > - self.interpreter.eliminate() > - self.interpreter.monte_carlo.error_analysis() > + self.interpreter.monte_carlo.setup(number=monte_carlo_sim) > + self.interpreter.monte_carlo.create_data() > + self.interpreter.monte_carlo.initial_values() > + self.interpreter.minimise.execute(min_algor=min_algor, > func_tol=self.opt_func_tol, max_iter=self.opt_max_iterations, > constraints=constraints) > + if self.eliminate: > + self.interpreter.eliminate() > + self.interpreter.monte_carlo.error_analysis() > > > def pre_run_parameters(self, model=None, model_path=None): > > 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=25358&r1=25357&r2=25358&view=diff > ============================================================================== > --- trunk/test_suite/system_tests/relax_disp.py (original) > +++ trunk/test_suite/system_tests/relax_disp.py Wed Aug 27 21:55:19 2014 > @@ -63,6 +63,7 @@ > to_skip = [ > > "test_bug_21344_sparse_time_spinlock_acquired_r1rho_fail_relax_disp", > "test_estimate_r2eff_err", > + "test_estimate_r2eff_err_auto", > "test_estimate_r2eff_err_methods" > "test_exp_fit", > "test_m61_exp_data_to_m61", > @@ -2746,6 +2747,86 @@ > > # Run the analysis. > relax_disp.Relax_disp(pipe_name=ds.pipe_name, > pipe_bundle=ds.pipe_bundle, results_dir=result_dir_name, models=MODELS, > grid_inc=GRID_INC, mc_sim_num=MC_NUM, modsel=MODSEL) > + > + # Verify the data. > + self.verify_r1rho_kjaergaard_missing_r1(models=MODELS, > result_dir_name=result_dir_name, do_assert=False) > + > + > + def test_estimate_r2eff_err_auto(self): > + """Test the user function for estimating R2eff errors from > exponential curve fitting, via the auto_analyses menu. > + > + 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. > + """ > + > + # Cluster residues > + cluster_ids = [ > + ":13@N", > + ":15@N", > + ":16@N", > + ":25@N", > + ":26@N", > + ":28@N", > + ":39@N", > + ":40@N", > + ":41@N", > + ":43@N", > + ":44@N", > + ":45@N", > + ":49@N", > + ":52@N", > + ":53@N"] > + > + # Load the data. > + self.setup_r1rho_kjaergaard(cluster_ids=cluster_ids, read_R1=False) > + > + # The dispersion models. > + MODELS = [MODEL_R2EFF, MODEL_NOREX] > + > + # The grid search size (the number of increments per dimension). > + GRID_INC = None > + > + # The number of Monte Carlo simulations to be used for error > analysis for exponential curve fitting of R2eff. > + # When set to minus 1, estimation of the errors will be extracted > from the covariance matrix. > + # This is HIGHLY likely to be wrong, but can be used in an initial > test fase. > + EXP_MC_NUM = -1 > + > + # The number of Monte Carlo simulations to be used for error > analysis at the end of the analysis. > + MC_NUM = 3 > + > + # Model selection technique. > + MODSEL = 'AIC' > + > + # Execute the auto-analysis (fast). > + # Standard parameters are: func_tol = 1e-25, grad_tol = None, > max_iter = 10000000, > + OPT_FUNC_TOL = 1e-25 > + relax_disp.Relax_disp.opt_func_tol = OPT_FUNC_TOL > + OPT_MAX_ITERATIONS = 10000000 > + relax_disp.Relax_disp.opt_max_iterations = OPT_MAX_ITERATIONS > + > + result_dir_name = ds.tmpdir > + > + # Make all spins free > + for curspin in cluster_ids: > + self.interpreter.relax_disp.cluster('free spins', curspin) > + # Shut them down > + self.interpreter.deselect.spin(spin_id=curspin, change_all=False) > + > + # Select only a subset of spins for global fitting > + #self.interpreter.select.spin(spin_id=':41@N', change_all=False) > + #self.interpreter.relax_disp.cluster('model_cluster', ':41@N') > + > + #self.interpreter.select.spin(spin_id=':40@N', change_all=False) > + #self.interpreter.relax_disp.cluster('model_cluster', ':40@N') > + > + self.interpreter.select.spin(spin_id=':52@N', change_all=False) > + #self.interpreter.relax_disp.cluster('model_cluster', ':52@N') > + > + # Run the analysis. > + relax_disp.Relax_disp(pipe_name=ds.pipe_name, > pipe_bundle=ds.pipe_bundle, results_dir=result_dir_name, models=MODELS, > grid_inc=GRID_INC, mc_sim_num=MC_NUM, exp_mc_sim_num=EXP_MC_NUM, > modsel=MODSEL) > > # Verify the data. > self.verify_r1rho_kjaergaard_missing_r1(models=MODELS, > result_dir_name=result_dir_name, do_assert=False) > > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-commits mailing list > [email protected] > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-commits _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
