Hi Edward. There is no scaling involved when calculating.
What I meant with scaling is correction to the co-variance matrix. Related to errors, or similar. But I haven't figured it out yet. Best Troels 2014-08-27 11:33 GMT+02:00 Edward d'Auvergne <edw...@nmr-relax.com>: > Does it give the same small result? Try turning off parameter scaling. > > Regards, > > Edward > > On 27 August 2014 11:29, <tlin...@nmr-relax.com> wrote: >> Author: tlinnet >> Date: Wed Aug 27 11:29:24 2014 >> New Revision: 25330 >> >> URL: http://svn.gna.org/viewcvs/relax?rev=25330&view=rev >> Log: >> Tried to implement the Jacobian from C-code. >> >> This though also report errors which are to small. >> >> Maybe some scaling is wrong. >> >> task #7822(https://gna.org/task/index.php?7822): Implement user function to >> estimate R2eff and associated errors for exponential curve fitting. >> >> Modified: >> trunk/specific_analyses/relax_disp/estimate_r2eff.py >> >> Modified: trunk/specific_analyses/relax_disp/estimate_r2eff.py >> URL: >> http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/estimate_r2eff.py?rev=25330&r1=25329&r2=25330&view=diff >> ============================================================================== >> --- trunk/specific_analyses/relax_disp/estimate_r2eff.py (original) >> +++ trunk/specific_analyses/relax_disp/estimate_r2eff.py Wed Aug 27 >> 11:29:24 2014 >> @@ -42,7 +42,7 @@ >> from specific_analyses.relax_disp.variables import MODEL_R2EFF >> from specific_analyses.relax_fit.optimisation import func_wrapper, >> dfunc_wrapper, d2func_wrapper >> from target_functions.chi2 import chi2_rankN >> -from target_functions.relax_fit import setup >> +from target_functions.relax_fit import jacobian, setup >> >> >> # Scipy installed. >> @@ -734,7 +734,7 @@ >> E.set_settings_minfx(min_algor=min_algor) >> >> # Do C code >> - do_C = False >> + do_C = True >> >> if do_C: >> # Initialise the function to minimise. >> @@ -766,19 +766,27 @@ >> param_vector, chi2, iter_count, f_count, g_count, h_count, warning = >> results_minfx >> >> # Get the Jacobian. >> - # First make a call to the Jacobian function, which store it in the >> class. >> - E.func_exp_grad(params=param_vector) >> - jacobian_matrix = deepcopy(E.jacobian_matrix) >> - >> + if do_C: >> + # First make a call to the Jacobian function, which store it in the >> class. >> + jacobian_matrix = transpose(asarray( jacobian(param_vector) ) ) >> + >> + # Compare with python code. >> + #E.func_exp_grad(params=param_vector) >> + #jacobian_matrix2 = deepcopy(E.jacobian_matrix) >> + #print jacobian_matrix >> + #print " " >> + #print jacobian_matrix2 >> + else: >> + jacobian_matrix = deepcopy(E.jacobian_matrix) >> + >> + # Get the co-variance >> + pcov = E.multifit_covar(J=jacobian_matrix) >> + >> + # To compute one standard deviation errors on the parameters, take the >> square root of the diagonal covariance. >> + param_vector_error = sqrt(diag(pcov)) >> # Set error to inf. >> #param_vector_error = [inf, inf] >> >> - # Get the co-variance >> - pcov = E.multifit_covar(J=jacobian_matrix) >> - >> - # To compute one standard deviation errors on the parameters, take the >> square root of the diagonal covariance. >> - param_vector_error = sqrt(diag(pcov)) >> - >> # Pack to list. >> results = [param_vector, param_vector_error, chi2, iter_count, f_count, >> g_count, h_count, warning] >> >> >> >> _______________________________________________ >> relax (http://www.nmr-relax.com) >> >> This is the relax-commits mailing list >> relax-comm...@gna.org >> >> 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 > relax-devel@gna.org > > 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 _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list relax-devel@gna.org 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
