Hi Edward. I am working right now at that solution. I will keep the structure in the __init__.
I think it will have a masked array in the target function. This is the test, which have been annoying me! test_hansen_cpmg_data_missing_auto_analysis 2014-06-10 14:11 GMT+02:00 Edward d'Auvergne <[email protected]>: > Hi, > > For reference, as missing data is quite common in real analyses, a > much, much faster implementation for handling missing data is > described in: > > http://article.gmane.org/gmane.science.nmr.relax.devel/5726 > > This would be orders of magnitude faster for this component. > > Regards, > > Edward > > > > > > > On 8 June 2014 22:22, <[email protected]> wrote: >> Author: tlinnet >> Date: Sun Jun 8 22:22:24 2014 >> New Revision: 23741 >> >> URL: http://svn.gna.org/viewcvs/relax?rev=23741&view=rev >> Log: >> Added self.has_missing keyword in initialization of the Dispersion class. >> >> This is to test once, per spin or cluster. >> This saves a looping over the dipsersion points, when collection the data. >> >> Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion >> models for Clustered analysis. >> >> Modified: >> branches/disp_spin_speed/target_functions/relax_disp.py >> >> Modified: branches/disp_spin_speed/target_functions/relax_disp.py >> URL: >> http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=23741&r1=23740&r2=23741&view=diff >> ============================================================================== >> --- branches/disp_spin_speed/target_functions/relax_disp.py (original) >> +++ branches/disp_spin_speed/target_functions/relax_disp.py Sun Jun 8 >> 22:22:24 2014 >> @@ -417,6 +417,7 @@ >> self.cpmg_frqs_a = np.ones(back_calc_shape + >> [self.max_num_disp_points]) >> self.num_disp_points_a = np.ones(back_calc_shape + >> [self.max_num_disp_points]) >> self.back_calc_a = np.ones(back_calc_shape + >> [self.max_num_disp_points]) >> + self.has_missing = False >> >> # Loop over the experiment types. >> for ei in range(self.num_exp): >> @@ -433,6 +434,10 @@ >> >> self.cpmg_frqs_a[ei][si][mi][oi][:num_disp_points] = >> self.cpmg_frqs[ei][mi][oi] >> >> self.num_disp_points_a[ei][si][mi][oi][:num_disp_points] = >> self.num_disp_points[ei][si][mi][oi] >> >> + for di in >> range(self.num_disp_points[ei][si][mi][oi]): >> + if self.missing[ei][si][mi][oi][di]: >> + self.has_missing = True >> + >> >> def calc_B14_chi2(self, R20A=None, R20B=None, dw=None, pA=None, >> kex=None): >> """Calculate the chi-squared value of the Baldwin (2014) 2-site >> exact solution model for all time scales. >> @@ -541,7 +546,6 @@ >> chi2_sum = 0.0 >> >> # Now return the values back to the structure of self.back_calc >> object. >> - ## For all missing data points, set the back-calculated value to >> the measured values so that it has no effect on the chi-squared value. >> # Loop over the spins. >> for si in range(self.num_spins): >> # Loop over the spectrometer frequencies. >> @@ -551,10 +555,11 @@ >> >> self.back_calc[0][si][mi][0] = >> self.back_calc_a[0][si][mi][0][:num_disp_points] >> >> - >> - for di in range(self.num_disp_points[0][si][mi][0]): >> - if self.missing[0][si][mi][0][di]: >> - self.back_calc[0][si][mi][0][di] = >> self.values[0][si][mi][0][di] >> + ## For all missing data points, set the back-calculated >> value to the measured values so that it has no effect on the chi-squared >> value. >> + if self.has_missing: >> + for di in range(self.num_disp_points[0][si][mi][0]): >> + if self.missing[0][si][mi][0][di]: >> + self.back_calc[0][si][mi][0][di] = >> self.values[0][si][mi][0][di] >> >> ## Calculate and return the chi-squared value. >> chi2_sum += chi2(self.values[0][si][mi][0], >> self.back_calc[0][si][mi][0], self.errors[0][si][mi][0]) >> >> >> _______________________________________________ >> 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 _______________________________________________ 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
